I think your instinct is absolutely right, and that will be the eventual reality. There are so many use cases: voting, AMAs, “dairy diary style”, to name a few. Each of these will likely need their own values for these settings in addition to new settings that don’t exist yet.
It would be technically easy to implement per-category settings for these. I’d like to make sure it’s easy for admin to configure this in a way that is not overwhelming.
Before that, the glaring hole is that there is no current way to backfill topics in a specific category to all be nested (in the UI that is, of course it can be done with direct server access). When you enable nesting for a category it only affects new topics, not existing ones.