I had looked into this recently.
The ALSA MIDI function to send a MIDI message takes a device UID parameter. It appears that if this is a valid UID, then patchbay connections are ignored and the message goes directly (and only) to that UID. There is no “connection” per se – only a parameter given to ALSA along with the message.
When you use connect instead of a direct device ID, then the message just comes out of the SC port from sources and is forwarded through its connections.
AFAICS, to use ALSA/JACK connections for MIDI, the MIDIOut object’s uid variable must be empty 0.
hjh