Is this not an issue about minimum equipment for IFR? Changing the rules about overflying congested areas involved no change to the aircraft (fairly obviously). However, flying IFR requires minimum levels of equipment under the ANO. Assuming the CAA are not about to throw out those requirements then many permit aircraft with their limited weight will have a probelm fitting all the kit and still leaving the ground.
I can't see how this will work unless the rules are relaxed to allow IFR using the new uncertified glass cockpit kit. Then we will have an issue of definition, i.e. when is a piece of equipment good enought to allow you to use it for IFR flight. The very process of some form of certification or approval is likely to add cost and defeat the purpose of having a modern permit machine. I would be interested to know how Experimental aircraft fly IFR in the US. Is it everyone for himself? If so, I can't see that happening in the UK or the rest of Europe.