This and disable any notification
Disable the stock SMS app's permissions.
Nope, that's not it. OPs problem aren't duplicate notifications, it's that some messages come through the stock messaging app even when you set Textra as your default, and some others come through Textra (and the ones that are on the stock one don't show up in Textra).
That's a very clear indication that it's RCS-related (as I've sadly come to learn on the V20). And since Textra doesn't have access to these (still not sure if it's a carrier-imposed block or if it's a poor Android implementation), those 'advanced messages' have to come through the stock app, even though it's not the default.
At least on T-Mobile's V20, the switch to turn this off is gone, so the only way to get all messages to come through Textra (and disabling Advanced Messages, so the other party won't see received/read/typing indicators) is by turning off VoLTE.