Mr. Morte,
With the UWPs generated by T20, my first idea is rendered moot; ignore the UWPs as broken.
Aside from the Marches and Rim, most of the 3I UWPs available have their roots in the wretchedly corrupt Genie files. The method by which the Genie data was generated didn't take into account CT's own sysgen, LBB:6 Scouts. (Mr. Thrash can explain this bit far better than I.)
I'd assume that the T20 publishers; knowing the broken nature of the Genie files, fixed those UWPs prior to publication.
Back to the problem at hand. Very interesting suggestions by everyone so far and any of them would make for an excellent explanation to you problem.
I'll leave aside the biological reasons; as good as they are, and suggest something different(1) -a sociological and historical reason.
T20 is set in M:1000. The 1st Survey was completed in 420 and the 2nd Survey isn't due for completion until 1065. IMHO and IMTU, the Imperium surveys constantly and the capital S surveys are simply baselines. Most, if not all, worlds have been surveyed at least cursorily since the 1st and 2nd Surveys.
The hi-pop 'hellhole' worlds of the pocket empire were founded about the same time the Sylean Federation morphed into the Third Imperium. The founding of the Imperium may or may not have been one of the reasons for that. Originally, the hellhole worlds were not hellhole worlds - or at least not as hellish as they seem today (1000). Their poor UWPs are the result of the hand of man.
The pocket empire is relatively new, founded in the last 200 years or so. Beforehand, the three hi-pop soon-to-be hellholes warred incessently with each other in a bewildering flurry of alliances, backstabs, and free-for-alls. Each of the worlds was damaged in these wars, either by enemy actions or the resource extraction and manufacturing efforts the wars demanded. The hi-pop worlds fought for centuries. Further colonization of the region was halted because colonies could not be adequately defended against the enemy(ies).
Then, Something Happened(tm). A new religion or an old one, a cultural shift, a shock from outside (my favorite), something, anything, happened and the wars between the hellhole worlds slowly sputtered to a halt. Perhaps the appearence of the 3I to spinward in the sector made the worlds take pause. Perhaps the appearence of the K'Kree to trailing did it. Perhaps it was both or a mixture of both with other events. Whatever it was, the hi-pop worlds decided to that it would be better to hang together than hang separately. They had far more in common than they did with anyone else.
This new 'pocket empire' was slow to take shape, the members had been enemies for centuries after all. A nice, long term project would help the empire grow together. Enter those three 'edens'.
Those nice worlds weren't so nice when the pocket empire formed or when the hellhole worlds were settled. They're nice now because of a two century terraforming effort by the pocket empire and they're still not really ready for large scale settlement. Of course, whether the empire can coax settlers from the 'hell' they know to the 'eden' they don't remains to be seen!
Summing it up; the pocket empire's M:1000 UWPs are not 'natural'. The hellholes are partially man-made as are the edens. The reason your pocket empire doesn't rule the region despite its large popualtion is twofold. First, the empire spends most of its funds on terraforming; terraforming those three worlds into edens and continually terraforming the man-made hellholes so that they don't get any worse.
Second, the empire's populace is decidely isolationist and pacifistic on the interstellar scale. They'll defend their own, they just don't want to be bothered with much else. Their own history, the very landscape of their homeworlds teaches them daily about the horrors of war.
Hope this blather helps.
Sincerely,
Larsen
1 - Why? Because someone proposed a biological answer before I could! Wahhhh!