"KATANA" binaries would be those compiled against the official Dreamcast SDK from Sega (usually just referred to as the Katana SDK). That would be the "real" difference between them.
Now, if you want to know why the fackue's program detects them as a Katana binary versus a normal homebrew unscrambled/scrambled binary, the easiest way to see that is to look at the source of fackue's BootDreams program
(since the 1st read checker source code that is available doesn't actually differentiate between the different types of binaries other than to say whether or not it is scrambled) and see what it is looking for. In the case of a Katana binary, it is looking for the following string somewhere in the binary:
shinobi library for dreamcast version
If the tool finds that particular string, it will report that it is a Katana binary (unless it detects that it is an ELF file first, but that's somewhat irrelevant here).