I do use full disk encryption, but when I'm logged in, any program that runs as me can access my files (subject to some partial restrictions that Apple introduced a while ago). And anyone gaining access to my unlocked computer can easily copy that password file.

You could say once malware is executed with my credentials it's game over anyway. But I disagree with that. Having a file full of passwords stolen is far worse than than anything else, including key loggers, because it's maximum damage in a minimum amount of time.

I want to make that as difficult as possible for any attacker.