Hey, there is usually two sort of foam inside these cases. The harder, denser stuff glued to the sides to keep your gear in place, and the way softer stuff that is used as you describe in the lid to press down on transport.
My experience is that on well built gear that pressure is ok. Keeps stuff fixated in transport. Often those blocks are not glued to the lid, but attached with velcro, so taking them out and cutting some of the top could be done.
Just remember that the foam should press down on the actual faceplate of your gear, the only way to get that done is if the knobs are sunk into the foam.
When you close the lid, without pushing on it, how big a gap is there?
Greetinx,
C.