Dan,
I agree with you. Which proves that like all rules, there is no clear cut demarcation based on any clearly defined criteria that makes one-side of a boundary anything much different that the other side, and there will always be examples to prove each side of the argument correct. Some group(s) will always feel alienated/ left out, no matter what is done.
The 12lb rule has served us well for years, even though there is nothing 'magic' about above/ below exactly 12lb. Adding the flap/ speedbrake requirement is a good thing to add complexity to the model.
Maybe the waiver flight should be more than just stick/ rudder/ throttle skills to fly a consistent landing - it needs to stress demonstration/ understanding of discipline towards flying and 'respect' and empathy towards the model, and not the 'casual' flying style that foamies promote/ encourage. That's hard to put into words suitable for a rule.
The responses from the JPO on RCG stressed the safety concern over lack of design understanding and building skills as the reason behind the DIY conversion prohibition for <12lb models. If that concern is real, then one proposal would be to introduce a Restricted Waiver and keep the DIY prohibition in that category only. That way, you don't stop experienced modellers with a Full Waiver from sensibly converting small models (such as the Freewing F-22/ Mig-29).
Paul