As far as the TU is concerned, those sysgen rules were never, at least in my ,mind anyway, really intended to do much more than produce 'cool' systems w/ earthlike planets orbiting gas giants,etc. And it all could easily be explained by all the 'meddling' that G'father & his clones did.
IMTU, it's *all* explained by Grandfather Et Al. Or - rather - by Some Really, Really Old And Powerful Civilization. I took the fact that the TU is two-dimensional (and thus significantly distorts real distances between stars) and laid out on a hexagonal grid to mean that in the universe of the game jump space is an artificial construct. NOTE: I also require that jumps take place only along the rows of the grid - in order to "turn" one must emerge from jump and then jump again in the new direction. Following from these "facts," I have the general rule that the systems populating the grid are 1) liveable (at least marginally), 2) junctions required to access the rest of the grid or 3) academically interesting. On a case-by-case basis, I tweak canon system data to the extent necessary to support this view.
In short, all of Charted Space (and everywhere else potentially reachable via the jump grid) is an artificial construct.