According to the man page F-FULLSYNC doesn't work with some firewire drives, is that the only limitation?
No. USB devices seem to have the same issues. In addition, some RAID controllers do not honor the SCSI SYNCHRONIZE_CACHE or ATA FLUSH CACHE / FLUSH CACHE EXT either. Why some bridges/controllers don't do this is not known. It could be because they never did an initial implementation. It could be because some website/magazine reviewed their bridge against another (which didn't do the flush either) and mentioned the performance was worse, so in the next revision they removed the support...Optimizing throughput at the cost of data integrity seems to be a foolish tradeoff. We have been working with many manufacturers to make sure their devices do this properly since journaling and other transaction oriented things (databases) require it.
The good news is, there is a workgroup part of T10 which is defining SCSI->ATA Translation (mostly for SAS controllers that will be compatible with Serial-ATA drives). However, we'd like to see the bridge manufacturers follow the guidelines established by this workgroup once the proposal makes it to T10. That will at least make things consistent across the board...
I know Dominic has said that it will work with all Apple provided drives but will it work with third party ATA drives?
Most, if not all, of the Serial-ATA / Parallel ATA drive manufacturers do the right thing today. For the most part, it's the non-bare drives that you have to worry about (those behind bridges, those in a RAID box, etc.).
-- Chris