Hard to say why. Why does LFL sign off on some really piss poor looking portraits for Diamond Select's UQS products but a great Sideshow portrait has to be changed to have Mace Windu's essence.
We know for fact that LFL had Sideshow tweak the Mace Windu sculpt, straight from the sculptor, and we've heard other things, not as conclusive, about them.
We just assume when Sideshow initially shows us one thing and it's significantly redone in production, odds are someone dictated it to be done.
The dome was practically perfect on the prototype, and the things that are different between the production and prototype are so significant, I really have to believe there was a deliberate change, not some mishap. So assuming that, I can't imagine why anyone at Sideshow would think let's change the helmet when it was perfect, the only reason I can think of would be if somehow it were easier to cast in production, not knowing anything about casting, that doesn't make much sense, but maybe. So, for me, all signs point to a deliberate action was taken to change the helmet and most likely it was at the request of LFL.