I totally agree that the team isn't built around him but I do think Guardiola makes some adjustments to the setup to allow him to flourish. He occupies that really specific inside right position to get the most out of his crosses, allow him to find spaces in between the lines, break ahead on counter-attacks etc. I think he also encourages a more direct style than Guardiola typically wanted from his midfielders. But the more interesting thing is how they were able to put Bernardo Silva in there instead and still be totally dominant, playing in largely the same way. Fernandinho was very good last season but Rodri looks excellent at initiating the attacks so it is a scary proposition.
People say Guardiola was lucky with Xavi and Iniesta or de Bruyne and Silva but he really provides the platform for them to dominate - there's a reason he's never had a poor midfield, beyond just the resources. Slotting in players like Busquets or Rodri might not have been unusual decisions (unlike putting someone like Lahm in there) but he knew how to make it work seamlessly. Most other elite teams have had plenty of midfield struggles over the same period.