Not sure what to say to that. My heels do ride very close to the cranks, but I also have my cleats set inboard. I don't have extra-long pedal spindles or extenders.
This is hard to deal with during a fitting session, because my foot angle only starts causing knee problems after I'm about 80 miles into a ride. I happily use SPDs on my commuter because my commute's not that long—although I'd still prefer to have a more toes-out stance there too.