Without knowing how QEMU does it, I'm guessing writes onto the emulated fat32 partition inside QEMU get caught by their software, and QEMU talks to Windows and says "Hello Windows, I would like to store this data as a file in this directory.". The directory can probably be on an NTFS disk or even Samba mount?

If a phone is "mounted" as FAT32, the writes from Windows should be intercepted by the driver and it would create Linux filesystem calls to create/write files. If an Android app decides to write onto that partition, there needs to be a program running on the Windows side to tell Windows' filesystem driver "Hey I'm going to create this file". Otherwise Windows will never see that file.

(I'm just guessing here, maybe there is a function to re-read the FAT?)