In general, fully featured PDF managers are expensive.
Well featured PDF editors aren’t cheap either - you can try free versions, but they all have disadvantages.
And they’re not markdown.
Highlighting a PDF can be done as an edit (ie it changes the readable/printable PDF) or as a layer (where the highlighting is contained within the program but the underlying PDF is unchanged).
Doing anything with blocks, requires text. If that isn’t already separated, then OCR will be needed. Same for line highlighting.
If you’re doing this for PDFs, there will be requests for doc, docx, odt etc (which Citavi also does).
And reference management, citing etc would another set of functions on top of all this.
It would take a humungous plugin to do all this.
What might be more feasible would be text scraping from documents (maintaining a link to the original file), converting the text into a markdown format (there would need to be a way to manage images), and applying block identifiers to blocks in the text. The plugin would need simple ways of adding notes and highlights. But I don’t see someone doing this in the very near future.
I do see this as a plugin suggestion rather than a feature request.