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It seems hypothes.is could be a solution to this way of reviewing with comments directly in the manuscript text. This is something I have often wished for when reviewing papers.
Several of the questions you pose are related to the proposal I posted here: http://www.sjscience.org/article?id=401. Your questions here actually make me reconsider my proposal. What if a review is not simply one coherent statement but a series of interactions with the author – a thread? I do not really think that fits into my proposed assessment model, but since this interactive review process seems a good idea I think it should. I need to think more about this…October 13, 2015 at 11:21 pm in reply to: Can we use base article-level research evaluation on open reviews and how? #2478
I also discussed this proposal briefly on Twitter with @michael_nielsen and @david_colquhoun. Michael Nielsen pointed out that I should relate my proposal better to the history of open peer review – previous efforts: his tweets. He has a good point and I think a good starting point may be this paper that he proposed: http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1000242.
David Colquhoun is somewhat sceptical – as I expected – but that was the whole idea of reaching out to him anyway. If this idea is any good I had better expose it to as much constructive criticism as possible to test and improve it. He has a number of good comments. I think all of them can be found here. One of the important comments he made is that in order to get a reliable assessment of an article, we probably need a substantial number of reviews of it. How would we attract enough reviewers? That is indeed one of the hardest questions.