If you are refering to the fact that the ports in the engine are much taller than the ports in the intake (center iron), then don't worry about it. This is by design. The stock intake was like that, as is the RB holley style intake.
FWIW, I have a GSL-SE 6 port engine using that same RB intake, topped with an Edelbrock 600 CFM (1405) carb, and it rocks. Even with 216K on the engine, it still runs strong.
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