I bought an ATX case because it was on sale and was cheaper than their smaller counterpart.

Only to realize that ATX motherboards are so much more expensive than micro ATX

So, my qyestion is what am I losing by opting for ATX?

And whether I should return the ATX case to get a micro ATX case for micro ATX boards.

Or keep the ATX case, and fit a micro ATX board? Or something else.

Because ATX boards, the cheapest one with DDR5 now is 300$.

Note: I'm going to put 4080 Super and 7800x3D (haven't purchased them yet, waiting for sale)

Normally a mATX board should go without problems in an ATX case, it'll just leave empty space around. But obviously fewer things can fit on an mATX board, fewer PCI-E slots for one, possibly also fewer M.2 and SATA, may also have fewer USB ports and so on. And elements may be more cramped together, so I really wouldn't advise a mATX MB for a top-tier video card, which is massive and hot.

The only notable difference is that it will be larger in size + weight (also possibly better airflow options depending on the case), other than that you won't be missing out on features that an mATX case would have. As for if you should return it, the best bet would be to compare the case you currently have with the mATX case you want to get & see if the extra size is worth it

As long as you can mount the motherboard onto the frame, whether it's mini or full sized or whatnot doesn't really matter. It's pretty standardized, even port layouts seem pretty standard with integrated peripherals.

Most commonly (but it's always better to check the documents) mATX motherboards fit to ATX cases. I've heard many using this setup to cut costs, but you should evaluate your needs. Smaller the motherboard means most usually less features, especially I/O ports.

When we are case shopping, what should we look for?
I just picked the one with most 5 star reviews and on sale. Do you have any recommendations for minimum # of ports or features to have that would make life easier?
I have no idea coming into this stuff.
But I plan to use it for gaming, might put a few ssd drives, a nvme

And a water cooling
Not needing any RGB. And maybe a dvd drive and a HD drive for storage.
I also have tons of external drives so having some usb ports would be nice
No need for WiFI.

Depends totally on your usecase, but with those needs I'd pick a ATX board.

This is very subjective. You don't need a case at all, your components would still work if they were just lying on your desk. That being said a good case can make your life much easier and can last for multiple generations of hardware, so it is worth to put some thought into it. Things I value in a case are:

1) Aesthetics: You'll have more fun with your computer if you like how it looks
2) Storage space: Does everything fit in, that you want to fit in? Even that oversized GPU, that third hard disk and that bluray player (a lot of cases don't feature slots for optical drives anymore)?
3 ) Ease of use: Do you need tools for everything or are the screws big enough to be tightened with your fingers? Are the edges polished or do you run the risk of cutting yourself?

Those are good criteria. With the bluray player, I use an external drive instead for that very reason. With storage, some cases only support 2.5 inch drives, whilst others support both 2.5 and 3.5. If you intend to have one or more HDD and not just SSDs, this might matter, since I think 3.5 HDD are generally faster than 2.5 HDD but I could be wrong there. I would also add the following, in no particular order:

1. Air flow/cooling: A 4080 super and 7800x3D will get hot so having a case that will keep it as cool as possible is advantageous. This largely depends on the number and position of fans, the type of fans and air intake vents, albeit you can replace fans if they're no good because there are standard sizes. Also, some cases come with fewer fans than they support so you can add more later.

2. Size: will it fit where you want it? Will it be heavy if you want to lift and shift? The latter can be a bit hard to avoid. Mine, with all the parts in, is heavy or maybe I need to hit the gym more :)

3. Quietness: this is important for me but not everyone and also goes with air flow/cooling because generally the better the airflow, the quieter the case is because it'll help prevent the noisy GPU and CPU fans spinning up too fast.

4. Number and position of front/top ports: do you need USB-C or is USB3 okay? Will your case be on the floor so top ports are better or on a table so front ports are better? One gotcha here that bit me: my case has a USB-C top port but the mATX board I got lacked a USB-C header so the port is currently unusable. However, like hmcpretender says, the case will outlive my motherboard.

5. Ease of keeping the interior dust free: ties in a bit with 1 in that you generally want positive air pressure. ie. more inflow of air than outflow to make sure that any dust entering the case is spat out and you want good quality filters in front of the intake fans to minimise the amount of dust that enters in the first place. This may matter less if you intend to replace your parts often. I tend to keep mine for 7 or more years.

6. Cable management: the better cases will allow you to route cables behind the motherboard, keeping the main area of the case open, which improves air flow and aesthetics.

GamersNexus case video reviews are useful. Even if they haven't reviewed the case you're looking at, they can give you an idea of what matters.

I actually chose an mATX board with a tower case due to cost and availability at the time. It wasn't ideal because I missed out on something that I wanted, in addition to the internal USB-C header but I can't recall what it was now. In any case, it was only a relatively minor thing.

One last thing, if you're less experienced in your build, too many criteria can be daunting so just try to pick the few that you think matters most. Also, I doubt anyone early in their journey bought the best thing. You learn from experience. My first case was terrible. Very poor air flow and a dodgy PSU.

Above all, enjoy the beast once it's fully assembled. Once you're gaming, you'll ignore any little inconveniences :)

Now I really want someone to tell us a story about that one dumb case :) On a related note, I think I had trouble fitting an expansion card bracket once because it somehow didn't seem to want to fit the slot on my case. Had to bend it quite a bit but luckily I didn't break it. I don't know if it was the case or the card that was dumb.

twistedpony gave a good thorough answer, but I want to stress that you need to check size, external size to see whether it'll fit where you want to put it, and internal sizes to see the maximum video card and CPU cooler size it will fit and make sure what you want will actually fit in it. Then the presence of external bays if you want that optical drive, because (bafflingly) most current cases no longer have those. Then decide on the watercooling solution you want and check whether it will work in that case. And also the positioning of the front panel ports, since if you for example put it in your desk like I do and the ports are on top they'll be unusable. Those are the make or break points.
And, of course, how it looks, you won't want a case you won't like to see. (Major problem for me because I generally don't want black around me and the vast majority are black.)
If you say you want watercooling, maybe the existing coolers and slots are somewhat less relevant, but generally airflow and fan slots, and built in fans, are another major criterion. And with such a video card and CPU, cooling is of huge importance, because those things will be HOT and you want to get those temperatures down as much as possible!
Internal bays should normally be sufficient in pretty much any current case, but should also check of course.

And, speaking of that, when you'll get the most expensive video card and CPU, I find it rather weird that you're skimping on what has to be a small percentage of the total cost on the motherboard. That puts everything together, and you also want it to be reliable, because it's the biggest pain to replace or have serviced. Anything else, take it out, put another one in. Motherboard, take everything else out, then take it out of the case, then put the new one in, then put everything else back on it.

Thanks for sharing everyone. I wish I could have all the parts in front of me and see if they all fit.
Sadly, I am still at the accumulating parts stage and it is my first build! :)
No motherboard yet as I'm still debating on the price. The case and board would already make it $400

About fans, do they come with the case? I bought 4000D at a sale and I don't see any additional fan pack in the package.

https://www.newegg.ca/black-corsair-4000d-airflow-atx-mid-tower/p/N82E16811139156

Only two front fans from what I can see in the photos

If you are talking about the Corsair 4000D:
The product page says the case is "Equipped with two CORSAIR 120mm AirGuide fans"
(source: https://www.corsair.com/ca/en/p/pc-cases/cc-9011198-ww/4000d-tempered-glass-mid-tower-atx-case-black-cc-9011198-ww)