Gmail's IMAP server treats "delete now" as "remove the label that corresponds to the folder".
It's always done that. And it's always been like that in Aqua, since this unusual logic is fully on the server.
The root of all this is -- GMail uses "labels" as its overall message organization concept, not folders, as all other mail services. So their IMAP server fakes folders (IMAP works with folders) -- and those folders are really Gmail labels.
One step to delete? Just Move to Deleted.
Gmail will automatically purges messages in Deleted which are older than 30 days, without any involvement from any mail app.
Or long press Deleted in Aqua from time to time, and choose Delete all.
With Gmail storage space being virtually unlimited, I really don't see how that would be wrong in any way....
And to reiterate -- "delete now" being treated as "remove the corresponding label" is part of Gmail's unusual logic of organizing messages.