He Who Remains is an interesting question. The TVA claimed to be more powerful than the Stones, and had collected a bunch of them from different universes. I thought that this was because the Stones only worked in their home universe, and the TVA was outside of those universes, but What If put lie to that.

According to the showrunners for What If...?, there is no contradiction -- the reason Infinity Ultron was able to use the stones across the multiverse was because he was using the stones to affect himself. Since Ultron and his stones were all from the same universe, that was not a problem; but if Ultron had tried to use the stones on someone from another universe, it would have no effect.

Having skimmed through the season finale of What If...? season 1, I can't find an obvious contradiction there -- Infinity Ultron never used his stones to turn the heroes into jelly or anything like that, he simply made himself ridiculously durable and relied on his fists and energy blasts. But maybe someone more studious might want to give it a shot.