this should now be possible with my beta (since b11) by using the new pdopts file.
in this you can specify pure data command line options which include :
-midiindev and -midioutdev
( should be possible with both ‘raw’ midi and alsa midi)
see: pure data command line for more details
ps. as far as I understand, the way PD represents thisin the patch is as a set of channels e.g. channel 1-16 = device 1, channel 17-23 = device 2 etc.
(hmm, good point, means on my new system, I should add midi channel to midi learn )
sorry, busy with other development at the moment, so don’t have time to get more specific examples, but hopefully this should give enough clues to get you up n running.