Yeah, that's what adding the foam does; suspend the PCB so the circuits clear the case, even when landing from jumps. Putting foam on the circuits themselves is next to useless IMO.
When I modded my case, I also created a slightly larger hole where the throttle wire exits and wrapped it in heatshrink to provide a little more shielding.
Yeah, having to mod the BEC is a bit on the extreme side of what a user should have to do to get a working controller. But if the choice is between a modded (but working) ESC, and an unmodded one that needs to repaired 4+ times, I'll take option 1.