Well, that’s a bit of a coy holdback, isn’t it. I suspect you’d better register attention for what you want by saying so, rather than ‘it’s broken’, or ‘I expect’ for unusual things.
Given Amber could see the special situation with many comments, I’d be confident it’s real, and will be on a list. Perhaps an upgrade for it will appear when the next Scrivener release does.
In the mean time, if I were doing a long thesis, I’d consider alternatives; and it makes me wonder whether embedded comments would even be the best way to go?
You don’t have to use Markdown to take advantage of all Obsidian has to offer, for example, including links, backlink, and graphics to help with relating items and even constructing networks. I suppose I’m thinking of excerpting chunks where you’re commenting at present, and using the [[ wikilinks-like ]] abilities to create and make notes, automatically attached.
I’m thinking excerpting this way because I don’t know that it would handle your entire thesis-as-text this way, but it might…
If Scrivener had the deep document links ability that’s becoming interesting in such arenas, there’d be a really nice way of doing what you’re attempting.
I thought about LiquidText, which has a recent much cleaned release I’ve been finding can be very nice for noting (and deep linking) on many forms of documents, but I wonder if it would keep up very well with particularly dynamic writing. It does have a level of abilities for updating an annotated document. I guess you could try it to assess level of usefulness.
So that’s some musing, and maybe as with other matters I’m personally working with, there’d be some advantage in diversity; perspectives from views of differing tools.