We appreciate you taking the time to try out the prototype and share your thorough feedback. I hope the time it's taken us to reply here does not signal the opposite.
Now, getting into the points you raised, a few comments and questions...
I would have expected to be able to edit the comment inline.
This is reasonable expectation. Currently, we are planning for this functionality to be included in v1.1. For context, the scope of this release is being defined in this ticket:T236916.
...the reply buttons didn't appear upon saving the page with the new wikitext editor...
This issue should now be resolved now that the new wikitext editor is no longer enabled on the prototype. If you are still not seeing the "Reply" links after saving an edit using full page editing, please let us know.
...the text box didn't appear when clicking "Reply" after going back to the "Read" tab from the "New section" tab (also with the new wikitext editor)...
Are you able to try this once more and see if the issue persists and if it does, let us know? ...I think this should now be resolved.
Firefox gave me the "data you have entered may not be saved" warning on closing the page after saving a comment.
Good spot. This seems to be happening to others as well. Here is the task where the work to resolve this issue is happening: T241393.
...the markup issues and inability to e.g. make a new section make it less usable in general due to the limited applications for which the editor can be used.
Markup issues: are you referring to the issues raised in "4." here?
New sections: How and when the reply workflow supports the creation of
== new sections == is something the team plans to discuss before v1.0's release. In the meantime, I saw you've expressed some thoughts around this on Phabricator (T241388#5766816). Tho, I wonder in what situations you notice yourself posting a reply and creating a new section in one edit?
Aside from DISPLAYTITLE, all of the magic words worked, which is mildly concerning.
Can you expand on this a bit more? My assumption is that magic words, like
__NOTOC__ __NOEDITSECTION__ __INDEX__ should work on talk pages and so it's expected that they would work if posted to the page using the new replying workflow. Although, I suspect you're aware of something I'm not...
...you can expect a response about the remaining points you raised  next week; I just wanted to make sure we got a start on these before any more time passes. Thank you for your patience and continuing help with all of this work.
1. Remaining issues to talk about:
a) Formatting resulting in a "list gap"
b) The content of a reply affecting the indentation of other content on the page
c) An infobox being indented at a different level of depth than the rest of the content the infobox was posted with
d) Inability to embed a table in a comment