For me personally I'd be happy to have default behaviour in which creating, checking and unchecking checkboxes affects only the currently selected bullet(s).
I recognise that others seem to prefer the current default, which is that creating, checking and unchecking affects currently selected bullet and all bullets below.
To accommodate both, I would suggest having an option that can be set (as for our current option to set whether clicking a bullet expands or zooms).
I'd be happy to have a way to remove checkboxes from sub-items but I don't see that I would ever use that and I definitely wouldn't want it to be the solution to the problem caused by the current default behaviour (if that is what you are suggesting?).
First - it creates an additional step (create a checkbox then remove all checkboxes automatically created at lower levels).
Second - I might not want to remove ALL checkboxes at lower levels. I'd presumably want to keep the ones I had deliberately created at an earlier date.
Hope I have understood correctly and that these points clarify my position. Please do come back to me if more info is needed. Hope this can be sorted soon - I would really like to use checkboxes as I write notes.