I think I've had the issue where Windows won't downgrade versions. ie. I had NTFS on the drive and needed to put Win98 on it. The Win installer refused to do so, and so I had to really wipe the drive to remove NTFS.
This was a while ago, so YMMV.
I can imagine the Windows tools lacking flexibility. But an fdisk and format (mkfs) should be enough to render NTFS presence "gone" - even though the data is still there.