Just to correct a couple of misconceptions here:
1. The entire cost of the ticket goes to the validating carrier. How the funds get distributed after that is up to the prorate agreement between the carriers involved. Many (perhaps most) of those agreements were negotiated before YQ/YR existed, so if the validating carrier decides to collect YQ/YR, then they may very well get to keep it. But it depends on the details of the agreement.
2. YQ/YR surcharges are not part of the fare rules. They can't be, as they don't depend on the fare - they're determined by the marketing carrier of the flights involved, not by the carrier who files the fare. When you see "surcharges" in the fare rules, that is a different kind of surcharge determined by the fare carrier.

I wrote a long post explaining the mechanics of these surcharges a while ago here on FlyerTalk:
http://www.flyertalk.com/forum/10048573-post166.html

Subsequently in the same thread somebody reported that certain European carriers will charge a "misplating fee", though it's not clear how widespread this practice is. I've never understood how either the YQ/YR or these misplating fees stood up to legal scrutiny (I'm just an engineer who implements airline pricing systems), but that is something to be determined by the lawyers, bureaucrats, and politicians.