So I figured the reason I have such a hard time with the underground pipes is that I can't see where to connect them to. I realized this is because I always build staff buildings near the main staff building (out of obvious reasons) and even if you switch to underground mode they don't get invisible.

I think they should be invisible at least when you are in the pipe construction mode (along with pretty much everything else).

A bit unrelated but I don't want to create new thread for every suggestion: Please also allow to show decoration quality on the coasters when not building them. It would be nice if you could see if the decorations you're placing are of any help without having to close the coaster (as you can add decorations without closing it).

And height marking on roads.