What a great bloody thread! I am sure the young fella/lass is getting something out of this. Nice to see such well-mannered and thought-out-responses. Of course, the brotherhood has always been superior in that regard (generic term that includes our sisters as well). It's all a good read.
Spit, don't over complicate the mission in respect of 328.3 and get 'too far down in the weeds' to start off with. These are the exceptions rather than the rule. You will find that similar exceptions exist the world over.
However, and just again in my experience, at a major airport the exceptions make little difference when dealing with passenger-carrying traffic; and, hence, basic capacity. I can't recall a single PIC of a large passenger-carrying aircraft waving ATC wake-turbulence separation minima (wake-vortex minima in your language) and take the responsibility. My experience may be different from others on that point but, in general terms, the pilots take what ATC tells them on this one.
In my view 328.3.31 can be a little misleading. The procedure in this country is 'sight and follow.' But I doubt you'd find a controller worth his salt that would assign a 'sight and follow' in a situation where the wake-turbulence standard would be compromised with RPT (regular public transport).
Consequently, I believe that in respect of your thesis wake-turbulence is a secondary issue. Not with respect to safety, but with respect to an overall postulation on runway capacity.
I'd suggest an 'addendum' to the effect that 'odd instances of pilot acceptance of responsibility for wake-vortex separation do not significantly influence runway capacity,' or something similar.
I will now retreat to the bunker after having cracked a very good Chardy and put the the tin-hat on.