A lot of this is probably obvious; circling back around to typical ways of running the wilderness, but through the lens of dungeoneering. Less a post about rules than about how to organize information.
Previously, I was thinking about 6-mile hexes as being like rooms in a dungeon. Now I think maybe they're supposed to be more like a 10' square. Hexes and squares are both the smallest unit of organization in mapping on their respective scales. You can traverse multiple per unit-time (turn in dungeon, day in wilderness), but it takes a unit-time to search either. They're also a unit of organization in your notes - you probably wouldn't have multiple encounters or multiple traps in a single 10' square in a dungeon, and you probably shouldn't in the wilderness either. I think the difficulty of book-keeping involved in trying to cram multiple lairs into each hex is a big gripe of mine with ACKS' assumptions about wilderness density. Yes, it makes sense in-the-world. But it's bad UX.
So if a hex is like a 10' square, what implications does this have?
"Rooms" / "biomes" / "zones" / micro-regions of multiple 6-mi hexes sharing common terrain, common opposition, and isolated by surrounding hexes ("walls"). Possibly a single key entry in DM's notes - "Cradle Wood, hexes 0601, 0602, 0501, 0503, 0504. Lush valley full of tall pine trees, ferns, stinging nettles, and moss. Abundant small creeks with crayfish. Three goblin villages (7, 5, 4 warbands) with wargs. Chiefs Ugbu, Ordo, and Glum are all brothers." And then you can vary random encounter tables by room - all demihuman encounters in Cradle Wood are goblins, or someaught. Weather might also be particular to a particular "room" ("Ironvale, hexes ... Valley in the hills where it rains most of the time. Oak trees and mud. Abundant iron and coal beneath the surface. Dwarven vault built into the hillside has flooding problems."). If naming "rooms" is too much hassle at scale, just number them like rooms on dungeon maps.
Vision - in the dungeon, the limit of your vision is by torchlight and measured in tens of feet. In the wilderness, it's by height and blocking terrain, and measured in 6-mile hexes, with a default of two hexes on flat plains. See also also Trilemma.
The function of walls in the dungeon, to block both movement and vision, is softened from boolean in the wilderness. Most terrain that slows movement also blocks vision (hills, forests), but some doesn't (open water, tundra). "Walls" in the wilderness are more like ridgelines. They're probably their own "rooms", since you can enter them - it'll just be slow going.
Does it make sense to have "unroomed" hexes? Sort of like hallways in dungeons, which are often unkeyed? Unroomed / unkeyed hexes might work well for "walls" too. Use default terrain random encounter tables to place dynamic lairs, assume low land-value relative to named and detailed areas. Sort of like leaving parts of your megadungeon to be filled procedurally during play.
Random encounter distance is one place where the analogy breaks down a bit. In the dungeon, a random encounter at book distances is unlikely to engage you for a turn or two. In the wilderness, by-the-book distances put them on top of you in minutes, definitely not days. I think it might be worthwhile to change random encounters to the "wandering monster / lurking threat" model, much like dungeon encounters - wargs picked up your trail and have been eating your leavings, elvish scouts have noticed your tree-cutting and are displeased, and so forth. So extend the random encounter distance to 1d3-1 hexes or so; sometimes you do stumble right on top of them, and for some random encounters that's the only time they make sense (skeletons aren't going to follow you, probably). My players have long complained about a lack of control over engagement in the wilderness, and having a little more advance warning might help. Might also be worth stealing a page from DaW's book and having an opposed Strategic Ability roll to see which side gets advantageous terrain before a wilderness fight, and then use the book values for random encounter distance to figure out how far apart the forces are at the beginning of the fight.
If a hex is like a 10' square, then microsandboxes need to be reconsidered. A 10 hex by 10 hex map is going to be very dense, without much room for rooms, much like a dungeon in a 10x10 grid, and my experiment with building such a tiny sandbox bears this impression out. So the howling emptiness of early D&D follows naturally from this metaphor - empty hexes are OK-to-necessary when hexes are considered primarily in clusters rather than individually.