Joey,
Well now you sound like you
ARE concerned with performance.
Are you familiar with engines like these inline fours that like to spin up high? You're right that the intake valve is still open during part of the compression stroke, which is why determining a true compression ratio is difficult. I could be wrong, but your approach here seems to be very car or big twin- oriented... Why do you think the cams are designed so that there is overlap on the intake and compression stroke? They didn't do it just so that the lobes look nice.
A nice port design will allow for a strong intake charge at high RPMs, which will overcome the compressing gasses and force more mixture in. YAt some RPMs compression suffers, others it benefits greatly. At certain points reversion is terrible. It's a wild cycle that can be described in many more than "four" strokes... but you seem to know the combustion cycle well. You gotta remember, it's all about getting that gas in there. Get good intake velocity, and those 30-something degrees past BDC aren't going to do anything but let more air and fuel in.
In any case, shortening the duration is not necessarily going to yield a higher compression. You seemed to give off the impression that port design and valve size, etc isn't all that important to your build, and now you're talking about cam profiles to get more compression. Anyway, don't let me be the Debby Downer... you have lots of fans here, so I'll keep quiet. I just like the go fast tech stuff. You know, what 754 said...