I tried Zotero and there was much I liked about it, but, ultimately, the non-native UI was just too much friction. (The same holds true for Obsidian.) I use Bookends to organize my PDFs of articles and books, and to generate bibliographies for work I do in Scrivener. I take notes on those PDFs in DevonThinks because it is, to be honest, freaking magical.
The way to do it is not to import your PDFs: leave them wherever Zotero or Bookends places them – Bookends just keeps them in a single directory in the iCloud Drive directory (because I sync with an iOS device) and index them in Devonthink. Then annotate them in PDF and DT creates a new folder called Annotations which, if you have added the links that DT lets you create, will take you straight to the spot in the PDF that is referenced in the annotation.
This is as close as it gets to blissing out while taking notes.