I find the ability to set hashtags on annotations and then sort them is already a great benefit over other markup apps.
I prefer apps to focus on doing well for their core strengths and inter-operability with other apps than trying to spread thinly across everything.
In this respect, I would prefer when MN would export its annotations rather than flattening them into the document. We could then use other apps (e.g. DevonThink) to search and categorize.
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JJW