Makes me wonder if the artist is going to pull a Mario 64 reference, have a epic battle scene, build up the climax and then end the scene with Bowsette picking Bowser up by the tail, spin around really fast and throw him into a bomb...
Although that might seriously damage a part of Bowsette's soul. Hmm...
It might not be a situation where Bowser extracts Bowsette and goes back to being Bowser; I don't think it's anything that simple. As bad as it'd be for Bowsette to go back to being Bowser, since she can't be Mario's wife in that form, this seems like it might have psychological stakes rather than physical stakes.
The Bowser seen here is probably a personification of the more brutish, arrogant and ambitious personality traits that Bowser had before he became Bowsette. In typical Bowser fashion, those mental aspects of Bowser's soul don't want to be replaced with the softer persona that Bowsette represents. Some part of Bowser still wants to hold on to the old ways, and doesn't want to go down without a fight. In other words, if this "Bowser" wins it doesn't mean Bowsette loses her human female body, but rather the old Bowser pre-character development gets control of the body and Bowsette takes the back seat somewhere dormant.
Also, I doubt that it's case of Bowsette is real and Bowser is fake, or Bowser is real and Bowsette is fake. Consciousness exists on many levels, and Bowser and Bowsette probably personify different aspects of who the original Bowser is at the moment -- signifying that his/her soul is at a crossroads right now. And yes, insert a Bowser is Bowsette's Persona/Stand joke as much as you want, because man would that be awesome.
I think she still has her Bowser skill set but is it enough to match the original
The usual trope here is that Bowser dominates Bowsette in raw brute force, so Bowsette has to win by, basically, being Bowsette instead of Bowser somehow - thus metaphorically reinforcing the idea that the Bowsette form is the superior one because it allows options the Bowser form can't match.
Power of Friendship/Love seems the likely sister trope here, since that's ultimately why she wants to be Bowsette instead of Bowser. And if that's the thing that gives Bowsette the win, it's quite possible that it'll take the form of Chompy helping. Of course, Chompy will have to get her relatively simple brain around the idea of who Bowser even is...