Revoke Profile without Removing App
I just checked the options on a 14.x server and it appears to be the same set of options organized under "Package Options". Based on that I think this would only affect the un-application of Packages and not the un-application of non-package based settings.
I agree with you about the Ghost profiles. I was looking to do something similar with the Cell APN that we are having manually set when our devices are provisioned.
It looks like SOTI is handling profiles without packages differently and the option is not available.
I can handle this by sending MX to the device. I was just surprised that it was missing, but as you have shown it is there when you add a package.
I admittedly do not like using that option because I like to be able to see what Profiles are actively applied and not worry about keeping track of any "ghost" Profiles that were maybe once applied.
With that said, the option is still there: