Yes you can save the settings… but requires typed a command in terminal. The settings are stored on the root filesystem which is locked. First you need to put it in read/write mode. Open a terminal by clicking the icon on bottom left of screen. Then type:
/root/scripts/remount-rw.sh
Now in Pd go to File -> Preferences -> Save all settings. Then you can lock the device back to read only mode:
/root/scripts/remount-ro.sh
Now it should always work, but it might depend on which order you plug the MIDI devices in. The MIDI device list is a little funky in Linux / Pd, which is why we defaulted to one device. Lemme know how it works!