ntfs is really bad (but it has 30 years, not really adapted now). and as usual for microsoft : undocumented.
as a general rule, underlayers on windows are old and depracated, particularly file systems.
however, the main issue with wine (and emulators using it) is that it doesn’t support certain technical requirements, thus, it may work, but not always, and genarally, people have issues with it.
btrfs is the best fs for me on batocera (it is not by default for a technical issue in the image builder tool). and more over, there is a driver for it on windows. you can format from menu > developpers > format a disk on batocera.
ext4 is good too, but as stated by the dev of ext4 himself, btrfs is the next fs generation, the future. technically, it is more adapted to recent disks technologies and usages.