Sounds like they weren't sure about Palpatine (or at least, Ian returning as Palpatine) until later into production.
If I understand what we eventually saw on screen: "Palpatine" was a spirit that could inhabit clone bodies. A culmination of all of the Sith knowledge and evil that had come before. So, the Emperor we saw in ROTJ may or may not have been the "original" body, right? Could have been a clone then. Either way, when Vader tossed him indown the observation tower, the Palpatine spirit unleashed went to Exegol, to inhabit a clone body.
...at some point, this was Snoke? is that right? (I'm still not sure if it was Palpatine in Snoke's body)
...and then when Kylo killed Snoke, the spirit went back to Exegol (although we did not "see" that happen in TLJ as we did in ROTJ)
...but this time the Spirit goes into an imperfect Palpatine clone body, basically reanimating a corpse?
Mike at RLM once postulated that the Exegol emperor was ALWAYS the "real" Palpatine, the man behind the curtain, and that the ROTJ Emperor was a clone of him (with appropriate dark side powers). But this does not appear to be the case, although I wouldn't mind if it were.