Oh I'm glad you like the look of Primal Planet so far!
Yeah unfortunately you can't adjust controls for the d-pad and thumbstick movements on a gamepad. I'm doing my best to make it so that players can cusomize their own controls on both keyboard and gamepad, but for now the d-pad is reserved for movement only and can't be changed, sorry.
You mentioned that you wish that there was a way to disable the Control section altogether, and just let the keyboard defaults sit as they are. You can use the default keyboard control setup. If you've changed it from the default setup, you can always reset the controls in the controls menu and just use the default control setup, unless I'm misunderstanding you.
Thanks for sharing this issue!