The lack of doors on the bottom wasn't an error, I meant to do it that way. So, I did this design like this because I was imagining the village to be outside of the mountain, on the edge of a canyon. The door on the bottom left, which you circled and wrote "cave system that takes you outside", is right, and that cave system would also be the way to get to the cavern entrances higher on the mountain. It would probably help if I designed and added in that to the map also.
Your edit to this isn't bad, and is actually really clever how you copied and pasted the walls, it looks surprisingly good
The thing is though, it adds in very much useless space, there's a ton of empty space at the bottom that has nothing much going on, it'd like to avoid things like that.
Later I'll put together another design that incorporates the tunnels to get to the village and takes into account the higher parts of the mountain.
Also, let's be a bit more specific talking about areas, I'm getting confused. We've got the village, here. There's the mountain, which has the east side, which is where you head up to Goron mountain, and the west side, which has the lava and mine carts. And the top, which you get to from the east side. When we say canyon, there are kind of several canyons so it gets confusing.
Let's hold off on sprinting this until we get the design planned out completely, the are still many other areas to sprite. Hyrule town's remaining interiors, miscellaneous interiors from the field and. Kokori forest and the swamp, etc.