Well, the USB stick itself won't be in anything - a partition on it might be. Linux itself is happy with a file-system written on the raw device. It's (probably) more normal to have a partition table, with one partition on it and the file-system on that, but there are DOS and GPT partition tables. Linux will find and use a fat32 file-system on any of these.
The relevant thing for a reflash is what the device bootloader can handle, and that is most likely to be the first partition on a DOS partition table.