If I understand the question, you're wondering if a particular cover hole should be matched up with any chosen stud.

Any way that the cover fits will work fine.  I always install my cover "level" but that's just because I put it back on the same way it came off.  In fact, I have always assumed that the holes & studs were not evenly spaced and that it would only go on one way, so I never even tried it at a different angle.

What really matters is that the gasket is pushed snugly up against both the engine block and the filter cover all the way around, with no gaps.

Speaking of gaskets, is that a home-made gasket in your picture?