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One has a removable plate (MMI) because some A4 installations take the exhaust out the other end of the manifold. The plate allows the MMI manifold to be used for either type of install. No idea why one hole is oblong.
As for which one to use? Well, if you need the exhaust at the flywheel end, the choice is easy. Otherwise, pick the one with the least internal corrosion. One of those 'pencil' cameras that work with a smartphone (cable or wifi) is a fun tool and not too expensive.
The joint between the manifold and the block shouldn't leak. And I don't recommend sealant there. If you feel compelled, just put it on the side of the gasket against the block. Put them together without any gasket and check clearances - something odd going on? Another check would be the length of the studs - perhaps they're too long (skim cut on manifold?). Some washers should help if that's the issue.
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