Man, I really need to know all the opportunities to earn bonus points, I think I am missing a bunch of them.
I can't give you all of them, because theres a good amount of them, but a few that i can think of right off the top are
1. the flower collecting level, collect extra flowers
2. any devlog has bonus and the first paralouge gives more bonus depending on the turn completion rate
3. the ninja level, if you spare villagers you get bonus