There is no built-in way to trigger a user-limited fetchmail run.
The Unit grommunio-fetchmail.service writes to /etc/fetchmailrc by default.
You could create a script/unit which writes a config/mailbox but then you still have to create something to trigger it.....
And to trigger a fetchmail call via send/receive from an client wouldn't really make sense as this is for the mailbox itself.
But a delay of say, 60 seconds shouldn't hurt any imapD.
And if a 2FA-Mail has such short ttl's than it isn't worth anything and should just die as there is no benefit in doing such nonsense other than saying "that makes it more secure". Probably a "manager"'s idea if at all.
I think you will have a better experience if you use a relay-host which forwards your mails directly to your grommunio-host via nat (e.g. a firewall-rule only allowing that host inbound on some port) or through a vpn.
You could self-host a proxmox mailgateway or look for providers as e.g. Cyren (whatever it was called).