"Low CR/high boost and high CR/low boost will both make 500hp and on the same octane fuel, but will deliver it differently. But that is a different point that I am trying to make."
If your engine parts are limiting you to 500hp, and you don't mind the expense of running high octane fuels, then yes, high CR is better.
The power delivery is better for high CR/low boost. That is why hoonin89 says it is better for track. I didn't think about this when we started this thread. Heck, if you can get to 500hp naturally aspirated, then that would be even better power delivery. Ditch the turbo, run high CR and high octane.
If getting more air thru your engine is the limiting factor (not the engine parts), then low CR/high boost will get you more power, at the expense of delivering it at later RPM, as turbos will do.
Your example of squeezing 500cc into 50cc is only using stage 2 of the engine. The turbo being stage 1, and the cylinder's CR being stage 2. So in your example, yes you do get more power as long as you don't hit the limit of the fuel's octane. Why would you run an engine at a lower than optimum compression level for a given fuel?
My proposal to run low CR/high boost will bring the compression level back to optimum for the fuel. The fuel's compression limit can be reached with both engines, but the engine with 70cc head volume can have 40% more fuel and oxygen than the engine with 50cc head volume. You just have to run stage 1 with 40% more boost, and be able to intercool that extra air. That extra fuel/air will spring back on the piston 40% harder. Both engines running the same octane fuel, same ignition timing... one engine makes 500hp, the other makes ~700hp. Yes the power delivery is more top end RPM, which makes it more challenging to drive. Turbos will do that, especially as you get into higher boost levels.
High CR/low turbo boost engine is just a middle ground between a NA engine, and a high boost turbo engine. Maybe that is why top fuel runs high octane and a super charger. Nice even power delivery and high power. Ditch the turbo if you want better power delivery.