Since the empeg sled is a hard-to-replace item, I would tend to want to protect it in favor of anything else. I'd mod the car before I'd mod the sled. You will be able to get a million replacements for the car parts many years into the future, but a replacement empeg sled is going to be a pretty rare item soon (already is, for the Mk1 sled).

If the player does not sit flush with the dash, I would re-do the bolt holes in the right place rather than try to cut the sled. In fact, it might be a problem because the docking connector needs to be at a certain depth to work properly.

If you do not like seeing the metal lip, I would suggest doing this trick from the FAQ rather than cutting the sled.