Potts (at least as far as I can tell from the movies; I haven't read the comics; please let me know if they take a different approach) is personal assistant to the cranky genius; her job is to go with him and help him do his next great project.
Shotwell is operations; her job is to take over the company the cranky genius built, keep it running smoothly and profitably, and let him go off and do his next great project.
Different jobs, both important. (It's a pity Musk doesn't seem to have a Pepper Potts, who might have talked him into giving up his Twitter account.)
I think this is precisely what Pepper Potts ends up doing in the movies. Tony Stark stops running the company. Not to condone the comparison or anything, just clarifying what happens in the movies.
I am not calling you out specifically... just think that her importance to SpaceX has been diminished and undersold and I think it due to: (1) the oversized spotlight that Elon commands and (2) Gwynne is a woman, and fairly attractive at that... and so multiple biases play against her.
(Comics are not nearly as original or modern as they'd like to pretend to be!)
Tony Stark is an arsehole, so is Elon.