The Gmail Spam folder is populated by Gmail. The Thunderbird Junk folder is populated by Thunderbird. My experience has been that the junk filter log applies only to filtering done by Thunderbird.

Thank you. That makes some sense. I guess then if I want my Thunderbird Junk filter to be sensitized to Spam, I've got to move everything that lands in Google Spam to Thunderbird Junk, and then I suppose Run Junk Mail Controls on Folder? That is, does the Junk filter act on everything that is in the Junk folder, or just on things that Thunderbird puts there?

Messages in Gmail Spam have already been determined to be spam. Messages in Junk folder were placed there by Thunderbird. Placing messages there intentionally would bypass the Thunderbird junk filter. The junk mail filter acts on messages received, tentatively, to inbox. It appears that you want Thunderbird to reconfirm the spam that Google identified? If that is your intent, you might consider setting a filter in Gmail to mark all messages as good, leaving it to Thunderbird to validate everything, but I recommend not doing that. This is a personal decision, and I hope my thoughts help you in your decision. I would leave it alone. Good luck.

Thanks again. That makes some sense. If Gmail is going to identify something as Spam, why should I worry about whether Thunderbird can identify the same e-mail as Junk. That being said, it is still useful to know that what goes in the Thunderbird Junk folder are e-mails that have already been identified by Thunderbird as Junk, and have already passed through the Thunderbird Junk filter. That is, manually putting e-mails in the Junk folder won't pass them through the Junk filter.

Now, I have other non-Gmail accounts. I guess it would be nice to train the Junk filter on those accounts to throw away e-mails that Gmail would identify as Spam. But I believe the Junk filters on Thunderbird are account-specific. That is, a Junk filter trained on Gmail in a Gmail account won't apply to e-mails on another account.

That is correct. Google does spam checking on Gmail messages, but messages in other accounts are not exposed to Google's filtering, but only to whatever its ISP filters, plus whatever Thunderbird filters. Consider that message flow is from ISP to Thunderbird, so having mail filtered by Gmail would require setting other accounts to direct their mail to Gmail - which can be done, but I don't advise doing it. That would give you just one account on Thunderbird.

I've just discovered this problem too. I found out that legitimate messages have been going into Gmail Spam folder, which is not the same as, and not viewable in TB "Junk" folder. To make matters worse, Google deletes "Spam" mail after 30 days. If you're not manually going into Gmail to check the Spam folder every 30 days, you could be losing e-mails.

I wonder how many business messages I've lost this way?

Edit: I see that the workaround is to subscribe to the Gmail Spam folder, so TB will import those messages. So you'll have a Junk folder and a Spam folder, but at least e-mails won't disappear into a Gmail black hole.

https://support.mozilla.org/en-US/kb/thunderbird-and-gmail#w_subscribing-to-folders-and-synchronizing-messages