You're not wrong. I still hope to get a better sense of how things play out along the Z-axis over the next few years.
(And Geoffrey Mandel and his support team on Star Charts should still be brought in as consultants in this.)
Reposted from the Trek Tech forum:
I noticed years ago that every map I have ever seen attempting to chart the Star Trek universe looks something like this:
Which is essentially a two dimensional projection from a "top down" perspective, assuming the Milky Way to be a relatively flat "disk", the thickness of which can safely be ignored. It's just 1000 light years, after all, and the Federation is (some would think) bigger than that anyway so you don't need to worry about thickness.
This has always bothered me on a fundamental way, not least of which because of the fact that in a disk 1000 light years thick, you could easily have as many as 500 stars layered on top of each other that would all appear to be in almost the exact same spot in a 2D map. If a number of those stars are inhabited or strategically important, that would make the "top down" projection less than useless for any practical purposes.
But after a couple of months playing Elite Dangerous and getting used to the idea of trying to navigate in the true vastness of 3D space, I happened to make a surprisingly long and annoying errand for remarkably wealthy tourist and I noticed something interesting:
Space is BIG.
You can actually stack several irregularly-shaped spheroid regions on top of each other in various complex arrangements, encompassing literally HUNDREDS of stars and planets each, and all of that with plenty of space in between (neutral planets for them to fight over) without going more than 500 light years from Sol.
It occurred to me, for example, that in my annoying tourist mission and the followup supply run that I had actually passed through systems controlled by three completely different governments in less than an hour. I was struck by the fact that if you were looking at the galaxy map from directly above the plane, this would seem really weird; the Empire, Independent and Federation holdings are more or less on opposite sides of the map from each other. But when you rotate the field and look at it from different perspectives you see they aren't "next" to each other at all, but actually wrapped around each other in complicated, winding blobs whose shape is determined almost entirely by how successful they are in holding on to systems in that region of space.
This is the thing that seems to screw up so many would-be start chart makers: the obsession with 2D. In a three dimensional galaxy, it doesn't take a whole lot of volume to encompass a very large number of stars and planets. The entire Romulan Empire could easily fit into a sphere just twenty light years in diameter and could still contain over a hundred stars and planetary systems; so, too, could the Klingon Empire still contain a huge number of stars and planets without actually being "large" in any absolute or relative sense. This would also explain why we can't figure out from dialog where the hell any of these big empires are in relation to each other and why it seems so weird that every major power in the galaxy somehow shares a border with every OTHER major power. It's because they DO, and because the sphere of influence of each empire are all packed together like pomegranate seeds inside the larger sphere of what most people not-quite-accurately refer to as "explored space."
tl;dr: Star Trek star charts don't make any sense when confined to two dimensions. They should quite literally have "ups" and "downs" in the scale of their various empires and one would expect that several of them would be "above" and "below" federation space while others are "next to" or even "wrapped around" it in some ways. It's also unlikely that any of these empires are going to have a regular, perfectly rounded shape or even be entirely contiguous: it could be common practice for governments to bypass huge regions of totally useless systems that consist of nothing but brown dwarfs and iceballs and then truck out sixty light years to annex a star with an Earthlike planet and then five of its neighbors for good measure.
