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Perhaps Readwise Reader with Obsidian exporter can do what you want.

// I capture entire webpage into markdown then annotate markdown.

I'm not sure if that is available out of the box, I haven't seen it if it is. But the killer feature of Obsidian is the community plugin ecosystem. I would be surprised if a plugin isn't available soon so make this happen.

There's the very good tool Hypothes.is for taking notes and highlights. If the Obsidian community can develop a plugin that can obtain the stream of highlights from the Hypothesis API, then I guess that is possible.