yes. the data can be stored on whatever filesystem you need it to. data saved to FAT can be saved to NTFS or any other file system. the file system does not change the file only how it is stored.
think shirts, red shirts are folded a certain way, and orange shirts are folded another. you can fold the red shirt like an orange or vise versa, the fold is the filesystem, the shirt is the file. you can fold it anyway you like, it always unfolds to be the same shirt.
greatly simplified explanation but I hope you get the idea