Or the sprawl could be created out of Mountainhome emmigrants, meaning they have distant relatives back in the Mountainhome, although if they emmigrated at the first generation, they may have unique traits to that nation, so that one particular village is the only place you find "flax-colored" hair because it was where the only two flax-colored haired dwarves in the whole Mountainhome went at the start of worldgen, and they interbred only with that one particular isolated village's population without really ever immigrating back to the Mountainhome, and only slightly with some of the other villages. A small hamlet set up by some of those decendents, however, might also be one of the strongholds of flaxen-hair-dom.
The reason this requires special consideration is because members of entity sprawl do not explicitly exist until encountered. Thus your suggestion is essentially impossible. It would, I suppose, be possible for historical figures to be removed from the general population with the explanation that they emigrated, and then their traits could be given to the members of a certain village. But this would be a lot of extra work and infrastructure, and the benefit would be small at best, while at worst it could end up with villages of near clones, and no similarity between members of different villages, even if they're members of the same national group and should be members of the same ethnic group.
So yeah, I don't believe that's a viable solution, nor would I consider it to be a good idea were it viable.
Actually, having isolated areas have very similar genetic traits with one another due to interbreeding of the same 2-3 families is a very realistic mechanic, and is simply the extreme end of the very "genetic similarity" effect this entire mechanic is supposed to create, so I have trouble seeing why you'd suddenly be opposed to it.
(And the less isolated a group is, the less it will have problems of a lack of genetic diversity.)
As for implimentation, this could be achieved without creating a huge backlog of individual historical figures by having a much less detailed "Historic immigration/emmigration flow" record. Rather than tracking individual dwarves (and their genes), you could have what amount to average rates of integrating populations, which create an abstract range of possible bloodlines for all the citizens of one particular area. The actual data on the bloodline only becomes hard data when a member of that bloodline is encountered. Until that point, villages are essentially just Shrodenger's Cat's Descendents, composed of proportionate amounts of possible bloodlines until you actually look at them. (At which point, the game rolls dice to see who, exactly, they belong to.)
If, for example, four families immigrated at Year 1 to set up an isolated mountain village, then there are only two families to draw genetic information from, and they will almost certainly interbreed repeatedly. If a citizen of another group immigrates in halfway through worldgen, and intermarries with that isolated village, and he was from a group that had 12 families largely stuck together, then, as long as none of those 12 families have yet been forced to be defined, he can have theoretical properties of any of those other twelve families as well (only some of which would have to be defined if you met this person, as there is only one exemplar of this entire bloodline unless you meet that original village), then, depending on how much further down worldgen you go, you could have this one thread of a bloodline also be added into the original four families, or you could have this bloodline only partially mixed in with the bloodlines of the original four if this occured soon before the cutoff date on worldgen.