Windows 3.x, 95, 98 and ME all used the DOS FAT filesystem (or the extended FAT32 variant). Windows XP supported both FAT and NTFS so if you did a clean install you were probably using NTFS.
What iOS 10.3 did was basically the equivalent of having a Windows upgrade which converted FAT/FAT32 to NTFS in-place without the user having to manage the process.
Windows XP did actually include a built in FAT32 to NTFS upgrade tool. Of course, you did have to run it manually from a command line, but I never had a failure from it. Vista would convert automatically if it saw a FAT boot drive, and I think Windows 2000 would upgrade FAT16 to 32.
I wonder if Apple will take the same approach for macOS (convert manually if you want for now, or we'll use it if you reinstall). Seems like a far greater risk for Apple if upgrading the OS breaks something for a lot of people, when they want users to be completely comfortable about updates.
It definitely worked on the boot partition at least on XP, not sure about 2k. If it can’t lock the drive it schedules it to be done at boot time (similar to on-boot chkdsk).
What iOS 10.3 did was basically the equivalent of having a Windows upgrade which converted FAT/FAT32 to NTFS in-place without the user having to manage the process.