Sorry, we meant for this to be documented more clearly: you cannot edit embedded attachments directly, embedding is intended for use with reference data (e.g., pictures or attachments from email messages) rather than for active documents. (What you can do, of course, is to drag your edited document back into your note to attach the newly edited version. But obviously that's an awkward workflow.)
We'd like to let you edit your embedded attachments, but there's a tough design problem that we didn't have time to solve in 1.0: it's really hard to coordinate editing correctly across multiple applications. The simple case isn't too hard (edit and save, you expect your edits to be saved), but what happens when you undo in OmniFocus while you still have the attachment open in your other application? Or vice versa? Which copy of the document is correct now, and how do they even know there is a conflicting version out there?
Your feedback is welcome, of course, and we do want for you to let us know if you want this capability so we know how to prioritize our work. I just wanted to explain that it's a known design issue, not just a trivial bug that needs to be fixed.