Yes. Thunderbird lets you control what happens when you delete a message.
If you open Account Settings for the account where it's not going to trash, then open Server Settings, there is a section with three radio buttons that is entitled, When I delete a message. The three radio button choices are:
1. Move it to a folder (followed by a dropdown that allows you to select the folder, which defaults to something other than Trash on your account's IMAP server).
2. Just mark it as deleted.
3. Remove it immediately.
If you have anything other than the first choice chosen, or you have the first choice chosen but have not set the folder to Trash under that Gmail account on the server, it's going somewhere else.
Brian - Windows 10 Pro, 64-Bit, Version 20H2, Build 19042
Always remember others may hate you but those who hate you don't win unless you hate them. And then you destroy yourself.
~ Richard M. Nixon