This is one of the reasons MTP was introduced for: independency of the file system format used "behind it". You can compare it to using "standard SQL" to retrieve data from a database via an ODBC driver: your application does not need to know whether there's a MySQL, Oracle, PostGreSQL, or whatever database behind it. As long as it sticks to standard SQL commands, it simply works.
Similar issue with MTP. Other than with using UMS, your computer doesn't access the file-system directly, but uses a kind of "command layer". On the Android device, MTP then plays the role of our above ODBC driver, translating everything to the underlying file system.
So as long as your computer knows how to deal with MTP, you don't have to even think about what file system is used. It should simply work.
But on the other hand, MTP has proven tricky sometimes: it requires extra drivers on Windows, and doesn't work out of the box on MacOS or Linux systems (also extra installs and adjustments required here). So there are alternatives you might wish to take a look at for file transfer, such as using apps like Airdroid, FTPServer, DavDrive, or similar.