Hi all, as Reader now permits downloads of PDFs with annotations, and printing of content within the app, I thought I’d record how that works with DT in case anyone was wondering and hadn’t got around to testing it yet. (Obviously this is as of 2023-04-02 - Reader is still in beta and with changes occurring regularly, so this functionality may change.)
Comments relate to web version of Reader on MacOS - unless I’ve missed something I couldn’t see either the export functionality or the print function in the iPadOS yet.
Print to PDF of web articles
If you already have hotkeys set up to print web content straight to your DT inbox, this continues to work in Reader (no reason why it wouldn’t since you do this in browser, but I’m just noting it).
You cannot summarise highlights made in Reader from the printed PDF imported to DT. Again, this makes sense, as this is an article that has been printed. However, it’s something to bear in mind. (I suspect this could be resolved with an “export to PDF” function so maybe Reader will address it in a future update.)
Downloading PDFs with annotations
The good stuff rubs hands with glee
It’s working perfectly. Downloading a PDF from Reader creates a proper PDF with standardised annotations 
Once the PDF is in DT, you can summarise highlights and it works as you’d expect, with both highlights and notes from Reader being “read” by DT. One little formatting blip (on the Reader side I assume): notes appear on the same line as the highlight they’re attached to in Markdown, rather than as a separate line (in the markdown they’re separated by only 1 return instead of 2, so when rendered they appear on the same line). Whether you care about this is down to personal preference and aesthetic (I prefer my highlights to stand alone, but I always edit my summary markdown so it doesn’t inconvenience me at all).
This means you can now read and annotate a PDF in Reader, safe in the knowledge that you can get your annotations back into DT to work with.
Annotations in the Inspector
I don’t use this function so I don’t know how people use it, but I know some DT people do so thought I should show it.
The annotation function in the second field of the Inspector in DT doesn’t populate (I don’t know if it’s meant to, I don’t know what it’s for!):
The annotations function in the fourth field of the Inspector populates with annotations (highlights and notes):
I haven’t tested any other workflows as these are the two that affect me, but if anyone has other things they do, feel free to post details here!
Although these are changes made to Reader, I think a thank you goes to both app teams for encouraging a standardisation in how PDFs are handled so that moving between apps is seamless 
I do wonder if they have realised the folly of that name, since you can’t google anything about the app without getting millions of hits for other things. (It also means troubleshooting is hard since you can’t google your question!)