You could make use of the script @troejgaard provided us. Define for example a category ‘Literature Note’ in the script – or if you’d use script for this sole purpose even leave the categorisation part out of the script and let the file name be created directly with [Literature Note]. The script opens the note, names the file based on the source file with the category in square brackets added to the end of the name and even puts a link to the created note file into the annotations file that is associated with the pdf.
While reading the pdf in DT, you could then invoke the script via Keyboard Maestro (or another application or via the script menu) and have the note file open alongside the pdf. Then you could copy the page link and paste it along with your comments in the created markdown file. You could tag the note file with your project identifier to easily find it again.
To collect all the notes, you could create a smart group that searches for both “Name contains [Literature Note]” and the Tag of your project identifier to have them all together.
I am currently trying to accomplish something similar to do research for my dissertation project.
EDIT: If you need the files outside of DT, you could index a folder from your file system and let a smart rule move (or even better: replicate) all notes with that identifier (+ the tag of your project if you want to narrow it down to only files regarding your project) to the indexed folder. This way the note files are even available to use “outside of DT”.
EDIT2: Sorry for the many edits, I was developing my thoughts while typing.