I downloaded Tarlia's clean versions of Strangetown and Veronaville but they removed all but a few townies in each for some inexplicable reason. In addition, I feel it would be a nice touch to have a desert neighborhood populated by Strangetown's townies instead of Pleasantview's townies like in every other custom neighborhood.

Is there a way to populate these neighborhoods with Strangetown's and/or Veronaville's townies and NPCs instead of having the Pleasantview ones or worse, randomly generated ones?

You would need to first set up your game with empty templates to stop the Pleasantview townies from spawning. Then using a copy of Strangetown with townies, go in and extract each one that you want with SimPE then clone them in Bodyshop. From there you can install them so they appear in CAS. Place them on a lot and use the cat teleporter or other mod to >make into a townie.