Yes, but the regulation covers maximum prices - it doesn't prevent operators from giving their subsidiaries lower prices. Though they're shooting themselves in the foot if they do, I think, as the EU would likely point to that and make it clear that it's either anti-competitive or a clear sign that the caps can be lowered further.

Sure, but it stop the problem (as an ancestor post says) of charging a subsidator X and charging others X×1000. Since X×1000 is capped, it's less of a problem.