As others have said.. cases back then were really, really, really iffy about having everything lined up properly.
Pretty sure out of the dozens of cases I had back then, only a very few actually lines up like they should have. Brand and weight mattered not for the most part.
And if all the holes line up with the board and you install the board without first installing a card to hold the board in place to make sure you could fit cards in after tightening everything down, you would most likely have issues with getting cards in there properly.
Even now, I usually just install the screws but don't tighten them down at all until i have installed a card and the screw to hold the card in place. It just makes things so much easier afterwards since there is always a little bit of play as far as the board being able to move around a little bit when not tightened down.