Observe that ouf riends at Ridgecrop Consultants make the source of fat32format available and tell us it compiles with MSVS 6.0, so that adding an option for the command line version to align FAT32 should be possible and it even might be possible to interest them on doing it themselves. But, at the moment, @jumper also has a working setup for compiling things with MSVS 6.0, so he also might become interested in creating an experimental version of it.