Pretty sure it uses EXT3/4. There is some difference in date/time storage between it and NTFS. You should however have no problem backing files from Windows to the MCM.
I handle my backups from the MCM to a My Cloud with an external USB using the Windows robocopy CMD. It works great and there is even a GUI interface you can download. It can easily be modified to backup from a PC to the MCM.
You can check out the batch file I wrote here.
