The problem did occasionally occur, but rarely. I remember a realm or two that had more regions than nobles. Those quickly fixed themselves, though, as nobles eager for positions moved in. The bigger problem was realms that just never appointed lords. Everything was centrally controled, and lords just reduced the amount of gold that was collected by the realm as a whole. Bankers moved all the food, and collected all the gold.
That's why the "no lord = half gold collection" was added.
However, realms controlling significantly more regions than they have nobles doesn't benefit the game much at all. Is BT really better off becauser Riomabra has twice as many regions as it does nobles? Or would it be better off if 12 of those regions went rogue, and some nobles moved in to take over those regions and make a new realm? Is Dwilight better off with Morek controlling the entire northern end of the continent, adopting a policy of leaving all of those extra regions completely devoid of infrastructure in a deliberate campaign to make settling the more difficult, or would it be better off if those regions went rogue, and a bunch of refugees from Luria resettled them into a new realm?
Morek and Riombara are NOT doing anyone any good for the game by locking up such a huge section of their respective maps for the benefit of a disproportionately small number of players. They are disproportionately strong due to the huge number of regions they control, and dominate their neighborhoods to the point where no one can challenge them. And since they don't have enough nobles themselves to split into separate realms, they stifle the entire region into stagnation.
IMO, it would be much better to force these realms into picking which regions they want to keep, and which ones they will allow to go rogue. 20 nobles controling 30 regions = stagnation. 20 nobles controling 20 region, plus an additional 10 rogue regions, is an opportunity for neighbors to expand. Or for foreign immigrants to move in and set up something new. Or maybe it's an opportunity for internal strife as the realm aregues over what should be kept, and what should be dropped. "You're not letting *my* duchy go rogue, I'm seceding to make my own realm!" In addition, those rogue regions will start breeding monster swarms, livening things up a bit.
