Even the Beyonder thought that noone could challenge his powers.
Thanos defeated Akhenaton,but Akhenaton had gained the HOTU from a different timeline.Tom Breevort has said that The End happened in an alternate reality.This is marvel's stance.This means that Thanos did not control the Multiverse,but only an alternate reality.Maybe there are other realities in which Akhenaton won,and other in which Doom succeded.Anyway to have power over the MUltiverse you must beabove it,not a part of it.When you introduce alternate realities you destroy the idea of power over the multiverse.
Thanos could probably overpower the LT because there are limits to the power the LT can employ in a single universe,as shown by what ifs or alternate realities in which he could not easily beat universal threats.
Furthermore,the LT uses M-bodies to manifest,and so do the other abstracts.They cannot manifest directly,and probably there is a limit to the power they can manifest through the m-bodies.
The Phoenix Force needs avatars to act because it exists on a higher plane of reality,just like the true Beyonders that can interact with our reality only through cosmic cubes.Did you see the True Beyonders in the End?Their universe was affected or not? Quite simply,they cannot be contained in the normal universe.
It would be like a human being trying to interact directly with bacteria or subatomic particles.In Nxm 154 Jean reformed the Universe and held it in her hands.And she was but one of countless phoenix avatars seen in the WHR,following the orders from the "voice" which was probably meant to represent God.
In the White Hot Room single Universes are seen as flickering points of light. In Morrison interpretation the phoenixes get incarnated to perform acts of microsurgery from the inside.When there is need of a "human viewpoint" for precision work.The M'Krann Crystal,if not repaired,would have destroyed all of reality😖o jean had to become Phoenix.Thanos ultimately returned everything to the status quo in which it was before;so there was no need to intervene.The voice/consciousness and the phoenixes exist outside normal spacetime,and can see everything from beginning to End.Therefore they know when a crisis will resolve itself or not.