The Multiverse has always existed. The Sacred Timeline was just a collection of realities that followed the same baseline although they had a few differences, for example, the main divergence in Classic Loki's timeline was that he survived, howsoever, the Nexus Event was Classic Loki deciding to reveal he was alive when in the main timeline he had not survived.
The Sacred Timeline is a collection of realities that is isolated from the rest of the Multiverse, one that has always existed. Now, the TVA sees the branches in the order they happen, right? So a branch in 2018 can be before a branch in 1027, but for the inhabitants of said universe, the branch in 1027 has to happen before the branch in 2018, although the TVA senses it differently, to beings like Uatu, the branch in 1027 is sensed in said year, and he senses the branch of 2018, 900+ years later.
So the TVA was pruning some timelines, while unknowingly other branches were existing. Paradoxically, the death of He Who Remains and the "birth" of the Multiverse in "Loki" is the reason why beings like Uatu, Ancient One or Deke knew of the multiverse and how branches happened all the time that could spin a new universe into existence.
The fake Multiverse in FFH doesn't mean the Multiverse did not exist (explicitly when we have been told in Endgame), a character lied about coming from an existing place, the lie was where he came from, not that the place he came from was fake.
The Disney+ order is because Loki begins immediately after his escape from Endgame while WandaVision is set 3 weeks after Endgame. And What If...? comes after Loki because although for inhabitants like Uatu the branches had always existed, these branches were paradoxically created after the events of Loki.