I don't think the TVA not dealing with Cap or Strange's exploits is a plot hole at all - in Loki Season 2 [spoilers!] the TVA undergoes a restructuring where their mission statement changes from preventing the creation of a multiverse - the reason they pruned Loki's time heist timeline - to PROTECTING the multiverse, mostly from Kang variants. Since the events of Loki started during the events of Avengers Endgame and likely concluded before the scene in which Cap returns the stones - and almost certainly before the events of Multiverse of Madness - then the TVA would have no reason to interfere with those things by that point.