How dare you not do lots of unpaid work to satisfy our whims?
I feel like the optimal solution would be 3, sort of. I would set a "master" doc, and that's where the inbox and stack would go to, but then allow searching across a directory. Most of what I want for multi-doc is the ability to surface tags across multiple directories ("Which projects have something due today?"), so that would work great for my needs.
That said, @robwalton, what you've made here is fantastic, I'm basically using it every day. I'm working on a post about the pros and cons of a multi-file system, I'm still trying to find a balance there, so this is still very helpful. I really appreciate the work you've done here!