Any mismatch (especially along the top and upper 2/3 of the sides) will create turbulence that may hurt performance. If the manifold is smaller and that causes the step, it's not a big deal really, and can help an overcammed engine at low speed (like idle and off idle). It will drop some power, but not a large amount. If the head is smaller than the manifold, it is akin to putting up a dam in a fast stream. On Edelbrocks, I find the CNC program can leave smaller steps and abrupt edges in the corners of the port openings that are not removed by hand at the factory. I use the same gasket I will assemble with, align it so the bolt holes are all centered in the gasket holes, then trace the ports on the head flange in permanent marker. I do this on the intake manifold too. I use marker because I dont like making scratches in aluminum with a scribe. Then I re-shape the opening to the tracing on both. I will blend the opening back about 3/4" on the heads to eliminate the things left from the factory. The intake I do the same deal, but I run it back at least an inch, more to 1.5" if possible, to make any change a smooth gradual one.
Edit: This technique only works when the intake is fit properly too...lol. I dont believe in enlarging blot holes or prying. If it dont sit right, it dont fit. Period.