Hi micha80
I am assuming you are referring to the personal user preferences. In this case, you could definitely create a custom section with leverages the REST API for reading and setting these options, as you say. However this is bound to require some significant development effort. If you are looking to do this, have a look at these calls .
What I would suggest however is to run trough your requirements with your Lithium manager. It could be that if you are just looking at removing extra (unused in your case) options, or re-arranging existing preferences - then this could be achieved with an engagement with Lithium Professional Services and ultimately require less effort.
Thanks,