Give it a spin and see how you get on! Off the top of my head, the only ones I can think of for sure are the animation for when Force Crush is used on him (which in all fairness you aren't likely to ever need to see since you don't fight him) and he has a new 'disabled' animation. Pretty sure there are a few more, but those are the ones that immediately come to mind.
Not that it matters now if the OP has it working in the game, but the reason for the error messages in MDLEdit appears on closer inspection to be due to multiple objects in the model file with duplicated names which seemed to be causing confusion on the animations side of things. I seem to have avoided this with my own version as I re-exported the new model from Max as Geom only with the HK Supermodel already referenced, so it didn't affect me. More to make doubly sure there wouldn't be any confusion/conflicts animation-wise due to my own paranoia than anything, but it appears to have been something of a necessary step. I also used MDLOps rather than MDLEdit.
I didn't realise that it would upset MDLEdit though, so my bad there.