allow to remove the mod docking ports on the parts that come with them fixed so you can combine multiple mods

KSP will not allow that. The game code will not allow for adding/removing of PartModule's at run-time -- thus, you cannot remove the docking ports from the parts while the game is loaded.

You can use a MM patch to remove them from the part, but it is not something that I am going to include. Feel free to research ModuleManager and how to create patches, and if you run into any SSTU specific problems, let me know and I'll see about helping you sort them out.