It really depends on how you are trying to do it. If you are simply trying to override the base histories, then you will run into this issue. This is fairly similar to overriding buildings. The game modifiers for both the original and the modded history are loaded at the start, thus both are being used by your sovereign. The best solution here is to simply create a modified version, call them rogue, war master, or dungeon lord, and apply your new modifiers to them. This may not be the most satisfying solution as it does not rid yourself of these other histories, but you are giving even more options in general.

Keep in mind you can override the unittype for the core sovereigns that have the bonus. So you can easily make a new bonus, then make the new sovereign unittype have that one instead.