Do you think it would make sense to do this conversion but put a layer of funky foam 3mm ontop of the black foam with the hole in it to protect the piezo?
Yeah, should work equally as well sensitivity-wise. Funky Foam is really cheap too so there's no harm in trying it. That said, the extra padding will probably increase the acoustic noise.
Personally, I don't really worry too much about breaking the heads seeing as I feel it's kinda unnecessary on an electric kit to be hitting with enough force to rip through a head and destroy a piezo lol. The only drum I'm remotely aggressive with is the kick, which I simply reinforced with a kevlar patch.