This is a category where the paid tools (Glasp, Liner, Readwise, Hypothesis) each work well for the specific workflow they were designed around, and badly for everything else. The mismatch shows up as friction — copy-pasting between tools, manually tagging things the tool should auto-tag, exporting to formats the next tool doesn't accept.
A custom-built research extension can be designed end-to-end around your actual workflow. Highlights export to your specific note-taking app in your specific format. Clippings are tagged by your own taxonomy. The extension talks to your knowledge graph directly. Built once, lasts as long as your research practice does.