Thanks for the contact. No, I don't know him, although I'd thought about contacting my embassy prior to embarking on such a trip. Never did though.
I didn't particularly feel that I was a 'special case' this time, as I was being rather randomly stopped at some checkpoints and equally randomly waived through at other ones. I don't think there was any logic to that. All in all I think I passed about 60-70 percent of the checkpoints on the Trans-Sah highway unnoticed.
In Salah was indeed a special case. Coming down there seemed to be no way to avoid having a guide. Coming back up I actually drove right through the checkpoint (with a guide in the car, but no one stopped me or even looked at me - there was no one at all at the checkpoint), but then at the camping in town the guardian volunteered to call the police to make sure I am officially registered. He said he would get into trouble for having an unregistered foreigner stay at his camping.
Each time I was stopped in Algeria there was the usual exchange of greetings and questions-answers, and only a couple of times I was actually asked to give my personal details. I handed out my fiche which was enough - hardly once or twice it was checked against my passport. No one ever asked me as to the nature of my invitation/visa - I don't think it matters at all in fact, definitely not north of In Salah. My friends (Algerians) who assisted me with the visa support were definitely not worried about 'getting into trouble' in relation to it.