I actually found an answer in the end in the form of:
sudo modprobe snd-hda-intel
I would never have guessed it, and I'm not sure if it's reliant on one or more of the packages I installed, however it seems to work on a fresh reboot, so it works for me. I can now start the patch, with audio, with a relatively simple...
pd-extended -open pd/test-tones.pd -alsa -nogui
I also had to add my user to the 'audio' group, but I had done that when I sent my first email.
check for security limits perhaps default account is more limited than on desktop?