It's better for the intake manifold side to be smaller. You don't want any kind of ledge that would disrupt air flow.
Like has been posted if the Manifold is a tad smaller then just run it and don't think twice! The Intake runner being smaller on the push rod side of the heads Intake port is actually the way to go ( helpful ) since that's one less point in the flow tract where expansion and contraction of the air stream to take place. Rule of Thumb is the less area's of expansion and contraction within the Intake tract, the wider and less peaky ( smoother ) the motors power band will be. This lip on that Intake port wall will also serve as a wet flow fuel shear on that outside wall . This will produce a better and more complete burning air and fuel mixture.
