I suspect your thinking about FAT as a general purpose filesystem rather than the uEFI System Partition (ESP). For the latter case, one simply serializes access to the FAT/directory and renames files into their final resting place. That is going to be as robust and uncorruptable as any of the more "advanced" file systems jouraling mechanisms. Sure you might have a lost FAT chain, or a FAT chain mismatch between FAT copies, but its not going to cause a boot problem and a FAT "fsck" operation done during boot is going to be the equivalent of throwing the incomplete journal entries away, and probably just as fast given most ESP's contain a less than a dozen files.

So, not a problem, with the huge advantage FAT can be implemented/validated/etc in a few dozen lines of code.

KISS