They're the same Ganon! At the beginning, he uses the bat Miraculous with Keese, but the goal of the Yiga (who he was raised in) is to find the Triforce Miraculous and use it to awaken the Great Beast. I haven't entirely decided how or where he gets it, but eventually Ganon does find the Miraculous of Power and with it the Kwami Din. I'm also not sure exactly what he does with Keese after that, but I don't think he gets rid of him or gives him back, but instead holds onto him. I definitely need to at some point design some combo designs for when the trio are using both of their main miraculous.
Also, just talking about this au bc why not: There would be section in the later part where the trio leave town to further their search for the triforce miraculous (although of course it's still sheikah vs. yiga) and end up running into a lot of different miraculous that are actively used in other places?