I agree with your assessment. “primary” — to me — implies one of many equally-important passwords. “master” implies a password that protects/overrides/controls all other passwords, which is what Thunderbird’s master password actually is.
By most estimates there are more slaves today than in any other point in history and it's almost entire in Eastern Europe, Asia, and Africa. Instead of helping those people, putting sanctions on the countries and companies turning a blind eye on slavery, or even acknowledging that slavery is not history but an ongoing condition - the West spins its wheels changing language in highly unrelated fields.
The absurdity of it all is something out of Camus.
Pirates were referred to as the "enemy of all mankind":
* https://www.penguinrandomhouse.com/books/545158/enemy-of-all...
* https://www.goodreads.com/book/show/52783845-enemy-of-all-ma...
Primary means it is the "main" one, but it doesn't imply any controlling relationship. It's kind of like "first".
Whereas "master" (in this context) means it has control or power over other things. For example a "master switch" would override all other switches. Or a "master cylinder" on a car controls the slave cylinder.
It's a real shame that they're making things less clear to fix an imagined problem.
As long as you are taking it at face value you will continue to be confused in this way, and you will continue to lose.
And beyond that, maybe it is because I am not a native speaker, but isn’t “primary” less clear than “master” in this context? `Master` suggest control/mastery over something, but `primary` rather focuses on importance/order of things, at least in my head.