It's certainly possible to set whatever you want as the frequency but it's not easy.

Just changing the bmminer.conf file doesn't work because it has built in software that resets that particular file randomly and you'd suddenly have a screaming heat machine again if you ignore it for too long.

So you make a copy of that file say bmminer2.conf and have the autorun script call that one instead (Not really sure where it is, but should be in the /etc/rc? somewhere, I did my own custom script and renamed the run files, so I didn't actually bother to find theirs to modify it.

If you're really daring you might want to call the conf with your own custom start script and disable the existing one. Also renaming single-board-test and bmminer in the /usr/bin folder to make sure only your script calls them and they don't start by some other process. As running some of those in multiple can mess with your PIC firmware and you'd have to reset them manually (Another irritating process to be sure)

Please be careful and do so at your own risk I almost burned up an S9 figuring out how to do it properly.

I'm running two autotune R4s (@533mhz) and an autotune S9 (@425mhz) with my modifications, and they will be happily set to wherever I like them and retain those settings after reboot. Stays cool even in the hottest of the summer if you go down as low as @350mhz or so, and in the cold of winter @550mhz+ but I like to change them with each season just to keep them efficient.

If anyone wants to run a development bounty for it I'll develop the process and code changes into an easy to follow format and post it for everyone to use. Perhaps even a script that'll do it for you if the amount is worth it. Only for autotune S9s and R4s with any version of the firmware, I haven't done it with any other models.