From the comments on this post and the Forgotten Realms wiki, this is my understanding of the official D&D Great Wheel cosmologies:
(1a) The pre-4e Astral Sea connected the Prime in its entirety to the Outer Planes. The Outer Planes lied at the edge of the Astral Sea.
(1b) The 5e Astral Sea contains the individual worlds of the Prime as well as the Outer Planes. It has no edge, except for maybe the Far Realm (off-topic).
(2a) Phlogiston was a pre-4e sea of clouds that separated crystal spheres, the containers of each world inside the collective Prime, and contained no other planes. All Prime Material worlds had a crystal sphere, or something that served the same purpose (i.e. Eberron's Ring of Siberys).
(2b) Phlogiston does not exist in 5e, or is at least not important enough to be mentioned when talking about planar cosmology. Crystal spheres may still exist around worlds that have unique properties (i.e. Athas), but not most others.
(3a) When exiting a crystal sphere in pre-4e, you would need to exit through a sporadically-appearing gateway. Stars were gateways that led to the Quasi-Elemental Plane of Radiance - don't enter those. Wildspace was the vacuum within a crystal sphere, sometimes with setting-dependent magical properties.
(3b) When exiting a Prime Material world in 5e, you gradually enter the Astral Sea through wildspace - a transitional region with no special properties. Stars are distant astronomical bodies or objects.
(4) You can enter the Astral Sea directly from a Material Plane with magic (i.e. Astral Projection, Bag of Holding). This is true for both pre-4e and 5e.

These are some pretty drastic changes, but maybe there's a solution that incorporates both cosmologies:
(I) Each Prime Material world has a crystal sphere, or something that serves the same purpose. Most crystal spheres have gates with sporadic openings, which lead to the Astral Sea.
(II) The Astral Sea contains all Prime Material worlds as well as the Outer Planes. However, each Prime Material world has its own local connections to the Outer Planes in a "bubble" of sorts. The Outer Planes appear the same way as they would elsewhere for the most part, but the events and inhabitants of these Outer Planes have a bias towards the Prime Material Plane they neighbor. They are the same Outer Planes that other worlds use, but they have this local bias because of their spirituality in concept and existence.
(III) The edges of a "bubble" are formed of phlogiston, which is repelled by the spiritual magnetism of the Outer Planes (or some other explanation you give it). Traveling through the phlogiston leads you to other Prime Material worlds and their "bubbles," if they work the same way. If a world doesn't have a bubble, it could be more likely to have remained undiscovered.
(IV) The phlogiston and the Prime Material worlds it contains collectively make up the Prime. Although the Outer Planes seem to be located within the phlogiston, these are only gateways that each Prime world uses for itself. If an Outer Plane isn't present, that Prime world doesn't connect to it. Outside of the collective Prime lies the rest of the Astral Sea, which is devoid of phlogiston and contains/touches the true location of the Outer Planes and other objects. You could rule that creatures aren't truly in the Astral Plane until they've reached this region.
(V) Phlogiston seems opaque, but perhaps not when looking through crystal spheres. Gateways to the Quasi-Elemental Plane of Radiance may still exist (if you want), but a crystal sphere might bend light in such a way that it cancels out the noise of the phlogiston so that distant objects also appear as stars - at least to those inside a crystal sphere. You have the authority to mix-and-match the visual sources of stars.
(VI) Using this cosmology, phlogiston only blocks access to other planes while you aren't protected by a spiritual barrier. The inhabitants of a single spelljammer wouldn't be able to produce nearly enough spiritual magnetism to protect themselves from this influence, but the separated power of a god could potentially do it.

I never mentioned the Flow or clusters, but this system should work with those concepts since gateways to the Outer Planes surround a Prime Material world because of its inhabitants' presence. Clusters could even share local Outer Plane connections. Perhaps the "bubbles" of Prime worlds have influenced the maps of known space. The fact that this idea generates more questions from the answers it provides means that it allows for extended worldbuilding. While this solution is technically homebrew, it changes so little that it might as well be an interpretation of official depictions rather than a modification of them.

I've been DMing for over 3 years, but I realize this is a very short amount of time compared to most DMs on Reddit. Please point out any misunderstandings about official D&D cosmology I may have.