Yes, amidiauto will reconnect every hw device to the first software port. You may edit /etc/amidiauto.conf rules file to customize the behavior a bit (search forum posts for some examples of the configuration). It does currently work with only the first port of multi-port software or hardware. We plan to add multi-port support for amidiauto in a future update.
Not sure if there’s other means to have the connections set up automatically. There’s always ‘udev rules’ you could create, like discussed here: Midi connection manager - they get executed automatically on various hardware events, like USB device getting connected to the system.