As someone who has also been a heavy Thunderbird user for years, I have not had the same experience. If anything, same content/subject/sender email spam is where Thunderbird's spam filter shines for me.
I have two fairly heavily spammed accounts, one of which has a public email address. They consistently catch and remove same or similar content spam every day without issue.
In regards to false positives, it does happen sometimes. Although in most cases the emails that end up in the junk folder legitimately resemble a spam message. Almost any time a legitimate email has been marked as spam, which doesn't really happen all that often, unspamming it is sufficient to ensure the sender doesn't end up there again.