Those 'top crossover holes' are actually 'dead holes' that lead to nothing. No exhaust will leak out, they aren't sealed or covered even with a factory intake.
As long as you used the correct intake gaskets for the 6X heads ('72 and later type) you're fine. The Edelbrock Performer intakes are made to fit both the '71 and earlier as well as the '72 and later style exhaust crossovers.
I know it looks like something's wrong. But everything's the way it's supposed to be.
You might try using the 'search' feature and type in 'crossover' or 'dead hole' and you'll see this same exact problem has been covered about a million times.