I would contest the points in the strongest terms - if your log man was TOLD to leave his engine running then he was complying with the law enforcement request as part of the check. He can easily say he WOULD have turned his engine off but for the "official" request by law enforcement to leave it running and any such attempt to issue points based on that should be considered entrapment and unlawful. I would ask WHY he was told the engine be left running as part of the checks (unless there were emissions checks or similar carried out at the time), as the engine running may have had no actual bearing on the tests and therefore your logman could and should have been allowed to turn his engine off to answer the call (as he knew he should) to avoid the penalty. I would also ask that the ombudsman also look into if there were other cases of points being issued by that particular copper under this same situation during those checks. Basically I'd make the copper sweat and justify any and all points given that day.
Any defense they may mount to the effect of "he should have asked permission from the copper" would be pure hokum, because :
A) it's extremely unlikely the copper would have been in range to get his attention while your logman's phone was ringing.
B) even if the copper was in range, pretty much anything sort of frantic waving and shouting by your logman would in all likelihood have been ignored by the copper anyway.
C) as stated already the copper TOLD him to leave his engine running thus denying your logman the choice to turn it off to answer the phone.
They cannot prove he would not normally have turned off the engine without being able to produce a detailed video log of his all his movements that align with his mobile phone activity log; which they won't have and would not even be able to get without a valid legal reason that he was under suspicion for a serious crime - and you CAN prove he was TOLD to leave it running, just tell them you'll take it to court and call the DVLA person as a witness who will not doubt attest the the fact the copper was telling ppl to leave their engine running.
Case closed.
( I cannot and I mean CANNOT abide hoity toity coppers, I've sadly met a few and they are half the reason there is so much crime; because dealing with these coppers makes YOU feel like the criminal, so people don't report crimes or come forward as witnesses.)
As to the "drunk driving" legislation, that is not the problem, again it's the coppers - my brother got nabbed for "drunk driving" when he went to the car to get something out of the boot around xmas, he sat in the car (as many ppl do) and popped the boot (broken lock), got the item, re-locked the car and was halfway back to the house, when he got nabbed by a copper who had been not 15 foot away, who tried to pin a "drunk in charge of a vehicle" charge on him, bloody well breathalized him on the path to the front door! - we managed to prove in court that the copper had seen him both get into and OUT of the car all in the space of a minute without closing the drivers door, turning on the engine or even inserting his keys - the case was dismissed.
Tell your log man to not roll over and take it up the tailpipe, because that's how bad coppers stain the entire force. (I don't hate coppers, I just hate the bad ones)
I've also witnessed a traffic warden about to attempt to issue a parking ticket to a car that had literally pulled up right next to me to go to the cashpoint, I saw the warden RUN ACROSS THE ROAD to get to the car - I told the warden the car owner was not 5 foot away and would be back in maybe one minute, and added if he issued a ticket I would act as a witness to contest it as it was a single and not a double yellow so he had a time limit to breach before a penalty was warranted. He walked off.
Edit: sorry for the wall of text - you touched a sore nerve