If chrome uses the same code for password storage as Thunderbird does then they have even less of an excuse for not allowing a separate Master password like Thunderbird does by default.
They do offer that, though. Except on Windows, where as I pointed out there is not decent built-in password/key management system and everything breaks down (forcing browsers to roll their own systems).
Thunderbird's master password system has nothing to do with the OS so I'm not really sure what you are talking about. I have to type my separate master password into Thunderbird in order to access those passwords in plaintext, regardless of how I'm otherwise logged in.
Again this isn't true on systems that have OS-supported password/key management.
For instance, on gnome-keyring systems by default the keyring is encrypted with your login password, and it's automatically unlocked when you log in and locked when you log out (or unlock/lock the screen). If you want to you can change the keyring password to be something different, then you have to manually enter it (a GUI password prompt pops up when Thunderbird or Chrome or whatever tries to ask for a key) to access things.
Thunderbird has nothing to do with that implementation, it just happily uses it. So do Chrome and Firefox. They all behave the same way. You can, in fact, store a password in Chrome and then retrieve it in Firefox or Thunderbird (or vice-versa) without having to do a re-import from one to the other, because it's the OS that's handling it all rather than everyone reinventing the wheel.
kwallet and keychain systems (for KDE and OS X) work similarly from what I understand.