The situation is muddied a bit by 4e content using its own cosmology with no continuity to Planescape, and then by 5e incorporating elements of 4e piecemeal while also attempting to harken back to the Great Wheel cosmology of pre-4e D&D (with a mixed end result I suppose, but more successes than failures I think).
5e's handling of Positive and Negative's positioning wrt the other planes unfortunately doesn't go back to the quasielemental planes as metaphysical border regions with the energy planes, but on the upside 5e seems to take a page of inspiration from Pathfinder when it alludes to the Feywild and Shadowfell as being influenced by metaphysical proximity to Positive and Negative respectively (as Pathfinder does more overtly with the First World and Plane of Shadow). Whether it's an overt influence or convergent design the end result is the same for the game play.
As far as timeline goes, the answer would be a lot easier if Planescape was still being retained as a primary source of planar continuity and history (which as of MToF seems to be suspect) rather than a very much pick and choose approach, likely as different authors are or aren't familiar with the original source material. The Planescape timeline would have had the Outer Planes developing first, prior to the appearance of mortal life, and the gods appearing later on after mortal belief began to change the landscape of the Outer Planes and worship caused the formation of the gods. The earliest outsiders would have appeared with those primordial Outer Planes (baernaloths/yugoloths, primordial pre-Spawning Stone slaadi, the pre-rilmani kamarel in the Outlands, and presumably entities of Law and Good never overtly named).
Planescape's planar timeline was heavily biased towards a focus on the Outer Planes and much of it had some in-character source bias in the telling, but the general scheme of things was there, studded with plot hooks like the chocolate chips in a giant cookie fresh from the oven.
The Far Realm has had a lot of contradictory takes over the years, but my favorite that I think meshes best with the original material is that it can be best considered as an entirely different cosmology only tangently interacting with the planes of the Great Wheel. It isn't antithetical so much as they're both hideously toxic to one another by virtue of possessing concepts that do not and cannot truly exist within the other. Think of them like adjacent soap bubbles of reality drifting atop the endless sea of possibility represented by the Deep Ethereal (a similar take seen by the Great Beyond cosmology's Maelstrom and the Abyss in Pathfinder as two competing realities grounded upon one another).
The precise timeline for the Inner/Energy Planes appearing is sometime -after- the early "pure" Outer Planes but prior to the creation of the Material Plane, as the Positive Energy plane is the source of those mortal souls that would ultimately produce belief and faith that would in turn mold the nature of the Outer Planes. I suspect some of the first outsiders might be seen as prokaryotes looking on in horror as early photosynthetic organisms / mortals produced oxygen / belief, leading to a metaphysical version of the so-called Great Oxygen Crises that forever altered the world.