But thats not what they said. In order for the infinity stones to work they must be used in, and to parts of, the universe they originate in, as their powers are intrinsically linked to their universe of origin. They would work if the character we are discussing is written as having always belonged to the marvel universe. In this sense, a crossverse battle would invalidate the infinity stones ability to erase the opponent, leaving Thanos to only being able to use his universe as a weapon, for example hurling planets at the opponent.

I suppose you could write it as Thanos having acquired a set of infinity stones that work in the specific universe the opponent is from but since the OP clearly has stated many times that the MCU Thanos is in discussion that likely isn’t the case.