Well, this was exactly what happened in 1876 when 3 states sent two sets of Electors to Congress. Because Article II and Amendment XII did not set forth what to do, there was a huge fight over it which was eventually resolved with an extra-constitutional compromise, putting a Republican in the White House (Hayes) while removing Federal troops from the former Confederate states, restoring them to full sovereignty.
Unfortunately for the Pence scenario, the Electoral Vote Counting Act, passed to prevent a recurrence, specifies how two competing slates are to be dealt with.
Yes, Pence can rule from the chair to accept Trump Electors and refuse Biden Electors - but it only takes one Senator and one Representative to appeal his ruling to the floor, where each Member or Senator present gets one vote, and in January 2021 (best case scenario) there will be 270 Democrats and 265 Republicans present.
There is no doubt that, if Pence were to do this, the floor would overrule the chair and count the Biden Electors.
Curious that the Governor would certify two different Electoral vote transmissions.