The To Do section in sidebar seems to show everything that has a checklist.
Is that how this section is supposed to work? Can I modify what shows up in the To Do section?
Can I modify what shows up in the To Do section?
No, but you can create your own smart overviews that meet your requirements.
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That’s correct. You can make your own.
For example, you could make a search to include notes with todo items (unfinished checklist items), and that also include the tag #important
That might be a way to make something more manageable.
I think it would make sense to make To Do to user editable. Then we can have a To Do overview that makes sense for each of us.
For me, the standard To Do is redundant - I have hundreds of notes with unchecked check lists, that are no longer relevant.
I’ve made my own version of To Do which excludes Notes that are Done - but I’ve had to give it a different name obviously. Being able to edit To Do to our own preferences would reduce sidebar clutter and confusion.
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Just to play devils advocate, what would you do if you had many forgotten or irrelevant “on the agenda” items? I would argue that the built-in search promotes good house-keeping. 
I think the built-in makes sense as a basis, but I also would have hundred’s of unfinished lists, and so I also don’t use it myself.
I think the answer is not to make To Do editable, because then it isn’t To Do anymore, but instead to allow people to hide things they don’t use in that sidebar, and create their own overviews, even called “To Do”. That is on the roadmap.
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That’s my experience! It’s also prompted me to use On The Agenda a bit differently - I used to use it to flag “stuff I need to deal with (soon-ish)”
Now I use a bespoke search on checklists, and use OTA just for
- Notes I’m going to work on today
- Newly created notes that I need to process