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Correct, that is, if the governor sends a separate slate (which has indeed happened a couple of times) THEN it is the job of the Congress and Senate in closed session to determine which slate to accept. Pence has no role, except to say, “There is an objection. The houses will now retire to address the objection.”

Well, that's not exactly how the Twelfth Amendment reads.
they shall name in their ballots the person voted for as President, ... and transmit sealed to the seat of the government of the United States, directed to the President of the Senate;--The President of the Senate shall, in the presence of the Senate and House of Representatives, open all the certificates and the votes shall then be counted;
So VPOTUS receives all of the ballots, certificates, etc. Since the legistlature has the plenary right to appoint the electors themselves, VPOTUS could simply ignore certificates from a governor contrary to those sent by the legislature. That can't be succesfully challenged in court. They could try to reject the slate from the legislature, but that would just neutralize those electors. They can't be flipped to the other candidate.

“VPOTUS could simply ignore certificates from a governor contrary to those sent by the legislature.”
No.
We have a Constitution.
That Constitution says he *SHALL* open *ALL* envelopes of submitted Electors.
“Shall” and “all” haven’t changed in meaning since our Founding LOL!
VP has NO discretion- maybe in your ‘living document’ world LOL!