I guess that's up to Steve if he wants to keep the PRO format proprietary. I'd bet that if ATP becomes a reality he adds support for it into APE (if it's worth his time maybe?).
There are some alternatives. Bob Puff's "floppy board" combined with his "pill" and "super pill" software make good copies of protected disks. They're not cheap but...
Also there are IBM 5 1/4" and 3 1/2" Atari drive emulator programs that would probably support the ATP format eventually (again a ?).
As long as people are still enjoying the old 8-bits somebody capable will hopefully continue to support those of us who are not real good at hardware and software design (I hope!).