To be honest I think the mechanic makes sense on Ifrit EX. Imagine you're Ifrit. You just summoned your nails. Let's say that normally you need time to charge up a Hellfire which is why he doesn't just drop nails and then Hellfire. You drop your third set of nails but the adventurers continue to attack you. You're nearly dead so you have no choice but to fire off Hellfire early and perhaps risk destroying yourself.

The Titan issues are just plain annoying though. It could be programmed around pretty easily by having the phase changes only occur after the Upheaval mechanic regardless of the HP check. That would mean some MBs would become unskippable, but stacks are nothing compared to two gaols up and Titan in the air. Only other thing would be to add extra HP checks within a handful of percent of the phase swap that would either cause a skip of the gaols or a swap for a different mechanic.