The fact that neither Froome nor Thomas was used as a leader in these first two stage races is certainly telling. If Froome is again asked to work for Bernal in the Dauphine, doesn't it strongly suggest that he will go into the TDF (assuming he does make the Tour team) as a dom, rather than co-leader?
Maybe Ineos will start the Dauphine with all three as leaders, but at some point one of them will emerge, and if it isn't Froome, how will his co-leadership at the Tour be rationalized? It seems to me that Froome is under great pressure to out-perform Bernal at the Dauphine, which means he's going to resist being asked to work for him. At best, he could be competing with Thomas for no. 2.
I think you also have to worry about how much time Froome lost at the end of the critical stages. Yes, he burned a lot of matches pulling Bernal, and maybe he felt it wasn't worth pushing for a relatively low position in an unimportant race, but Jumbo had riders working for Roglic, and three of them finished in the ten slots behind him. Sivakov worked for Bernal at Occitanie, and still finished a close second behind him. Froome worked for Wiggins in the 2011 Vuelta (up to a point), and in the 2012 Tour (some might call that up to a point, too), but still managed to finish on the podium. It's possible to work for a leader and still finish high.