Theoretically, it shouldn't. Then again, mkfs.vfat shouldn't create a nonstandard FAT32 partition, but according to that Windows 10 thread, it seems that it does, so who knows? If it's running dosfsck on boot and whenever you disconnect your Kobo from your PC and you did the reformat using that partition program and things are still working fine for you using the Windows 10 Anniversary Update, then I suppose everything is fine.
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