It appears that Villagers are only appearing as the villager.png file, with the overlay for professions and biomes not appearing in game while using any texture packs that change villager skins. 

I have tried this with multiple texture packs and ran into the same issue with all of them. additionally, I have verified that the textures for the overlays all appeared as .tga files and that they were routed correctly as well. I had others test this as well outside of the beta and not run into the issue, so this issue is directly related to the beta version of the game. 

I will note that it appears that these overlays are applying, just not appearing in game. If you save and exit with villagers in the screen, the thumbnail for the save file will show the villagers with the overlay applied. Only, when you load back into the game the overlays are no longer applied and you are just able to see the villager.png skin file again with no overlays whatsoever.