Having read a couple of the cited cases and the council's response in this case, I suggest a different approach.
IMO, the legal issues here are:
Even if a Traffic Management Order includes provisions that a 'clock' must be displayed in a time-limited BB holders' bay(which I think is permissible), is the traffic sign prescribed under the TSRGD adequate to convey this requirement and would its use meet the council's LATOR duty; and
Even if it did, would the use of the contravention description '...BB in the prescribed manner' be a permissible means to demand a penalty?
IMO, no and no.
1. TSRGD are clear as is the requirement to request the SoS's approval to a varied sign;
2. No. The mandated penalty refers to terms defined in legislation (i.e. BB and prescribed manner) and it does not lie with the council to, shall we say, broaden the meanings of either so as to shoehorn a contravention of a TMO into the mandated penalty grounds.
And IMO there's procedural impropriety in the PCN i.e. the mandatory warning regarding 'if reps are made but a NTO is still issued the owner must respond to the NTO' seems to be missing.