I believe I am going try try swapping those entry points so it uses 1 and 3 instead. Otherwise I'd have to touch every single village (none have them set properly that I've seen yet) to add those two entry points. 1 and 3 are usually used for bandits raiding the village, so the two start far away from one another, but I think it should work decently.
Villages will always be 1 and 3 now. Towns use different entry points, but I've not heard of any issued with being attacked by bandits in towns as of yet, so I'll leave that alone.
Manually adding entry point 2 and 4 now. 1 and 3 don't work properly because of the mission template data. Rather then risk screwing something up by modifying those, I'll just add the intended entry points to each village scene.