1. That's good idea and I had scenarios in my mind, but decided to leave that for full game, if I ever make one.
2. Yes, it's random, but not deterministic , which means when you quick-load, you get totally different random order when adding new hex prisms. I plan to make that an option.
3. I didn't want to make complete sandbox because i thought that was one the biggest problem with Townscaper, but would sandbox mode, where you can pick your own color solve that? Right now, the player can do that by modding the save game.