The rationale behind using MTP is that "in the old days", the android device had to unmount its "/sdcard" partition and hand over the block-device to the PC, that mounted it just like any single-partition usb-stick. Downside is, that a) the PC mounting the android device could arbitrarily corrupt the filesystem structure and b) all programs accessing the filesystem on the android side needed to shutdown, and c) you only could use a filesytem well supported by all major computer operating systems: hence FAT.

MTP doesn't work on the level of a block-device, but rather works like, e.g. "rsync/scp/sftp over USB". So the Android handset can leave the partition mounted, all program can stay running, any filesystem can be used on the handset side, and potential for data corruption is minimized.