I think you're encountering one of gmail's idiosyncrasies. In Gmail, there is really only one folder. Thunderbird downloads to inbox and moves them to spam folder.

No, what's happening is Gmail is moving the phish to spam, but Tbird is downloading it anyway. Can you set Tbird to just download what is in the Inbox?

What is happening it you, like many people, assume the inbox is where pop mail is downloaded from. The standard actually uses the term maildrop and in most circumstances this is what passes as the inbox as the inbox contains new mail and can be considered synonymous but not always. Google are offering ALL new mail to the pop client, not just the inbox part because all of the new mail has arrived in the maildrop.

No, what's happening is Gmail is moving the phish to spam, but Tbird is downloading it anyway. Can you set Tbird to just download what is in the Inbox?

No you can not. POP has no concept of an inbox even, let alone phishing or spam folders it has a maildrop where all mail received for the address is to be found. Some providers do not follow the standard and hive off spam from what is offered for download in POP. I spent time with a very frustrated individual yesterday because their provider did not offer spam so they were forever messing around in webmail to get false positives into their mail client by marking mail as not spam. For him IMAP was really the only choice as that downloaded all the server side folders, but it would have been a far superior solution if the provider had just offer the maildrop content without imposing their own non standard take on email. If you are curious that provider was "the messaging company" they might meet your wants better than Google who are apparently following the standard.