- Almanac is a list of labelled map features. If you don't want a specific city (wood, mountain range etc) to have a label on the map, "remove it from the almanac". In the same way you can add a map feature to the almanac.
- Toponyms are unreliable, sometime they get rerolled when they shouldn't it. It's a bug, but at the moment it is as it is. Changing the Style settings do not get toponyms rerolled though.
- Same as the previous point.
- Saving any custom changes (custom names, added settlements etc) is a more complex task than it may seem. I don't think this will be implemented anytime soon, but I do hope to fix permalinks.