3 is a result of Gmail's imap implementation, and can be squarely blamed on Google. They did this intentionally. Instead of mapping the your tags as imap labels, they mapped them as a folder structure.

While it certainly shouldn't be necessary, I do feel like it should be possible to work around this in a mail client, however; don't emails these days all have unique ids? If not, storing a hash of the message content+headers/timestamps for every message should be enough to keep a local index of what each message is tagged as (given the implementation where each message shows up in multiple places). I can somewhat understand Thunderbird not wanting to make compatibility shims for specific vendors poor implementations.