You could use InDesign notes. A script could be created to convert the notes to the annotation layer you describe.
even better, you could use indesign's Conditional Text feature, that was specifically created for this exact problem (i think the official documentation actually used a teacher vs student edition of a document to illustrate how to use it)
So you could covert the note to a text box with applied Object Styles? Then, you'd have to be able to convert them back to Notes again to hide them...
The notes would go to a disposable layer.
Conditional text is better, no script required.
Hmmm...I like how Conditional Text is working. Since I can put an Anchored Object on it's own layer.
I think this is worth playing with.