Neil, I'd leave the hex head bolts alone, no countersinking. Our resident set of "becklocks" on Beck's buggy have been pounded pretty good and the bolt heads really don't show any wear. It doesn't seem to hurt to have them sticking out. Well, maybe a little pain in the bling but that's about it.
Welding skill is key, and with 32 3/8" bolts, you don't have to worry about coning, hitting them, etc. There's so many extra that a more stress on them won't hurt a bit. TR's work fine with 20 5/16" bolts.