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You're probably better off sending your specific questions to the list, so we can quote them in our replies and discuss them.
IMO the notion of "tag-based email" is misleading to begin with. I would call both notmuch and mu *search* based email tools. Tagging is just one small part of it.
<pre wrap="">The last time I checked, the main differences between notmuch and mu were in threading, community, and spinoff tools. I think the handling of threads is superior in notmuch (YMMV), and this is particularly visible in the emacs interfaces. The downside of that is slower indexing. Notmuch has a wider developer community while mu is mostly a one man show. Notmuch has more people to keep the project moving, but one person might provide a more unified UI experience. Finally, I think there are more tools and MUAs written around notmuch, partly due to the language bindings to the library.</pre>