I hope that all ATC documents state something like this.
"Nothing in this part precludes a controller from using discretion and
initiative in any particular circumstance where these procedures appear to be in conflict with the requirement to promote the safe conduct of flight."
Safety is the primary concern.
The UK MATS Part 1 Certainly does:
Nothing in this manual prevents controllers from using their own discretion and initiative in any particular circumstance.
This is an interesting debate. Even though this is class G, so no standard separation is applied, the fundamental purpose of an ATC service is to prevent collisions between aircraft in the air. By applying the height stop, the ATCO is fulfilling this responsibility. I would expect that when you are no longer in conflict they will remove the restriction.
ryl