The next step is to have settlements placed in sensible and/or game-appropriate ways. Like
not having nearly every single stronghold in the game sitting out in the middle of nowhere
It sounds like the 6000 plots could be used to build complex subregions; if we were to make a continent out of a map like this, and made it, say, twice the size of Dwilight, each region could have, on average, 12 subregions. Lords could then take those subregions and divvy them up into estates.
(Or we could try and implement that BM 2.0 idea you had, where you start out at the subregion level, and agglomerate subregions together arbitrarily to make regions...but that's probably impractical
)