If you decide to do this, I would take the ESC out of the case before you start drilling.
Personally, this just lets in more dirt/dust and shouldn't be needed, especially if using a UBEC. And if running the MM that hard where the bottom layer is overheating, maybe the MM isn't the right ESC to use. IMO, extending the pins that connect both PCBs (to create a larger gap) and then adding a heatspreader would be better.