Let me clarify for the both of you.
Quick answer, yes. Independence is not prejudice to the method of jailbreaking, nor does it utilize SSH when uploading ringtones.
As for the matters with SSH:
Battery:
You can download a variety of programs to control the running processes on the iPhone through installer.app. Services, and NetServices (which is what I use) work just fine. This allows you to turn on and off the service as needed, in order not to draw unneeded power.
Multiple SSH Servers:
I strongly discourage the frequent installing and uninstalling of the server. And when you install a second SSH server, to the best of my knowledge it replaces the first, so there is no reason to keep uninstalling it anyway.
Recognition:
It is also true that Independence does not recognize that an iPhone has SSH installed, except for after it has installed SSH itself.