When I built a new computer this summer, I did at least one thing that was, at least in principle, wrong: buying the case before the motherboard.
It turned out okay, because the board fits the case well enough, if not perfectly, but what if I wanted a board that didn't fit? I might have had to get a different board, but considering my inexperience, I would more likely have bought a board before I knew how well it fit the case. With those case sizes--ATX, micro-ATX, etc., it may be hard to get a board that doesn't fit at all, but the various shapes of same-profiled boards still cause some uncertainty.
And the principle seems appropriate: since the motherboard is more important than the case, the case fitting the board is more important than vice versa.
I was trying to build from the outside in instead of from the inside out.

Well, you really need to pay attention to video cards. Not all video cards will fit in all cases; in fact, that is the card that is most likely to get you into trouble when it is 1/4 inch too long to fit without interfering with a drive bay at the front of the case.

An ATX mobo will fit in a case that is designed to handle an ATX mobo.

My mobo has integrated video.

As long as you don't want to play all the newest games, that's great. But if you ever wanted to upgrade to an add-on video card, case space is very important. And that 1/4 inch of space you don't have is always what gets 'ya!

Exactly, and such small differences are within the limits of the profile sizes, aren't they? Which seems to validate what I learned.