ATC have an inbuilt pucker factor when it comes to aircraft getting too close together. Regardless of the strict application of the rules they will apply separation or segregation when necessary. The rules often don't keep up with the changing traffic dynamics.
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.