I would love for Agenda to remember how I manually sorted my notes in a project, so that if I autosort them by date, I can quickly go back to how I sorted them manually.
Not fully understanding this. Agenda does record your manual sorted order. That is actually the only order. However, when you attach a date to a note, it does enforce chronological order with other notes that have dates.
I guess you are asking to be able to choose the sort order of the notes. Not sure we will do that. Agenda is pretty focussed on the idea of a time line. If you would prefer to have fully reorderable notes, you can do that by simply removing the dates.