I was wondering if Pillars of Eternity will combine the expansions into a single package installer, much like The Witcher 3 did. I tried looking online, but did not see anything. Just wondering if someone else may know.

I doubt it. There's too many variations of the game already (Hero Edition, Champion Edition, Royal Edition, Kickstarter Editions + White March Part I, Part II, Expansion Pass). Combining them into GOTY Edition(s) would be nightmare. Damn, we still don't have an upgrade options between existing versions!

And is that a "real retail version", or just a steam installer on disc + a code in a box?

For a digital release, does it matter that much if it's one installer or 3?

A Steam key.

For me that's the reason why I skipped it so far and I hope for a GOTY edition - a version that includes everything gameplay relevant. Maybe then there is a a goty special edition with extra goodies (back- or sidestory eBooks, audio commentary, development story). I just want an installer which includes the whole game and I don't need to check what's gameplay-wise the best version for me and which expansion works only with which version.

Always? Or is there sometimes a note saying "better luck next time"?
(thanks for the information, please don't take my sarcasm personal)

These days, if a company releases a joke of a boxed game then I won't even buy their digital version at full price. Yep, also referring to PoE II - I haven't even read an official statement that says that the DVD just contains the Steam installer. Are you talking about the GOG release? The (GOG) expansions work with any (GOG) version of the main game. Do you have an example of another (GOG) game where that's not the case? If not, I don't see your point.

Thanks to everyone for their replies! :)

The point is that you need to spend some time for research and check everything before you buy something. An example is Sword of the Stars: The Piit. You needed to install the DLCs/expansions in the correct order to get the it work properly. I'm not sure, but I believe there was at some point also the problem if you skipped one expansion. And yes, I'm talking about the GOG release. I believe they fixed that at some point with upgrading everyone with some DLCs to the gold version. But as you see, with many different versions and expansions everything can easily become confusing, at least for me. For that reason I prefer easy solutions, which means GOTY versions that includes everything.