Linux should be able to read any floppy/CD you create in Windows.
Linux is able to read/write a great number of filesystems (format types). The only Windows filesystem Linux has trouble with is NTFS. The specs on NTFS are proprietary and closed, and Linux developers have to guess at them. But floppies, which are usually FAT, and CDs shouldn't be any problem.
You might be able to format a floppy as NTFS, but I've not heard of anybody doing it.