I used exFAT with retroarch until i read how Nintendo Switch file structure works.
I went to copy my NAND Dump to my PC a few days ago and the second file was corrupted. Most definitely due to exFAT file structure.
With exFAT, there is only one file allocation table. When a file is opened and the system gets interrupted before the file closes again, the FAT loses its index of where that actual file is, and it becomes unrecoverable forever.
The same thing happens with FAT32, except FAT32 has two file allocation tables, and when one of them becomes corrupt, it uses the backup to restore.
No matter how careful you are to never go directly back to the home screen, or how hard you try to close the current file, something outside your control WILL eventually happen for you to get file corruption with exFAT on the Switch with Retroarch.
exFAT works fine on OFW on the switch, something to do with the journalism system it uses and corruption doesn't become an issue (I can't remember how this works, plenty of info via google).
I went through the pain of going back to FAT32 on the MicroSD, i use a exFAT usb plugged into the dock to install games over 4gb and it all works like a charm, with peace of mind my MicroSD isn't likely to get corrupted.