Disney Dan brought up a great point in his video on the closure: The Villains show theater has two theater boxes on either side of the stage with screens in them, and the walls of the theater (at least the walls around the stage and half of the side walls) have screens as well. They could easily put Muppet*Vision back as a screen-only version, with the animatronics being screens and such. Not sure what you'd do for the penguins or Sweetums, though. New screen segment under the main screen for the penguins, and maybe overlaying Sweetums on the screens on the wall or Penguin orchestra screen? But if Disney doesn't scrap the animatronics, it is really that expensive to reinstall them? Can't be any more expensive than developing an entire new show like Villains, TLM, or the upcoming Monsters Inc show. I have zero knowledge on budgets though.
Also, I'm willing to bet Disney does a DCA PhilharMagic and the MuppetVision theater will be entirely the same for the Monsters Inc show going there, just with Muppet decor removed and the theater box curtains closed, animatronics or their components still sitting there.