I think that’s happen because pop3 connector (getmail) pushes the downloaded mail directly in the INBOX folder.
I haven’t tried this howto with a configuration like yours but you try it:
You can safely ignore the last part where you have to modify the db (unless you have to manage groups too).
After you create the template-custom, remember to go in the pop3 connector dashboard, disable and reenable one (one is sufficient) of the pop3 connector that you have created to activate the template-custom.