What I'm talking about is how the game engine represents 3D space, and how engine capabilities enable and constrain game design.

> 3D is an illusion in this sense in every game, with the potential exception of space combat simulators.

In almost all general-purpose game engines, most game objects are modeled as 3D polygonal meshes and placed in the world using three coordinates. They can be scaled and rotated freely. The world can be viewed from any position and angle and with any projection (disregarding some of the limitations imposed by rasterization). Object movement and physics are continuous and handled uniformly regardless of direction. Whether or not this is an illusion is a question of philosophy, but I can't think of a way this could reasonably be more "real".

> And they can only make it work by pretending inertia doesn't exist.

This hasn't been true for decades. The Elite series has done this since the 90s, and the latest entry Elite Dangerous implements physics-based space dogfighting with momentum and inertia, though you need to disable Flight Assist to get the full simulation. For a more grounded simulation, Kerbal Space Program implements enough orbital mechanics to support satellites in different orbits, and is realistic enough to enable many real-world spaceflight techniques. And I also have to mention Outer Wilds and its small solar system with simulated spherical explorable planets and moons. All of these games would be fundamentally impossible without 3D.

> You can fly in World of Warcraft, but all of the content is on the ground, and the designers keep griping about how they don't want you to fly because it makes them feel bad when you skip their content.

This is a statement about Blizzard's game design, rather than anything fundamental about 3D. Yes, giving players the ability to fly requires a different approach to world design. That doesn't make WoW any less 3D. You can have a bridge, and one player can walk on it while another is under it. And a third player could be flying over it with a flying mount.

> You can jump in Quake. You can't jump in Doom. This makes no difference. Level layout is the same.

Doom levels are 2D with added height information. Quake levels are actually 3D. This imposes many fundamental limitations on Doom level design. You can't build a multi-floor building in Doom where you can see down to the previous floors. You can't have a pit in the middle of a room and leave the pit via a tunnel, because you can't have two walkable surfaces laid vertically on top of each other. You can't walk on top of a building and then enter it, or have floating platforms, walk under a bridge, have a spiral staircase that overlaps itself, etc.

> Elevation is real in both games; you can always walk up a ramp. There are three dimensions whether you can jump or not.

Doom has heights, but it cannot represent arbitrary 3D geometry, only a very limited subset.

RuneScape is somewhere between Doom and Quake, with its own set of limitations. While the game uses actual 3D models and therefore can display any 3D shape, much like Doom the world consists of top-down 2D levels with per-tile & object height information. The game does enable "rooms over rooms" by having up to four floors / layers per tile, used for things like multi-floor buildings. The player can't walk between floors; they must use an object like a ladder, a portal or agility shortcut to teleport to another floor.