The bottom fan is purely for cooling the HD as far as I can see and as that area is pretty much cut off from the rest of the case, and the psu aids in extracting hot air from the hard drives, I don't think the bottom 120mm fan contributes hardly anuything to case cooling.
That leaves 3 fans - So in stock config. Lian Li have 1 fan blowing air in from the top, and 2 fans extracting air (one near rear of cpu socket), and one near gpu.
What I am thinking is that with these huge cpu heatsinks, all the top fan is doing is blowing air onto the heatsink which blocks it from doing any other components any good (NB for instance) and then it gets extracted by the rear fan almost straight away. Plus even if you used a stock intel heatsink and cool air was able to dissipate into the case - I always thought the idea of having 1 fan as intake (top fan) and another as an outtake (rear fan) so near to each other creates a shortcircuit in the airflow. The cool air from the top is being extracted as quick as it gets into the case. Would it not be better to do what most other case manufacturers do and have both the top fan and rear fan as outakes so hot air gets drawn out. This is the way most people run their TJ09 and Antec P180's and it works.
The only thing I see wrong is the gpu cooling. Again in the Lian Li it is set to extract hot air. The TJ09 blows in cool air onto the gpu's as does the Akasa Mirage thermal sidepanel, as does the Antec P180 if you add a 120mm fan in the upper hard drive cage. The Lian Li does the exact opposite. I suppose you could argue that cool air gets warm from the gpu's and rises in the case and the top fans have to do more work. So better to have the gpu fan extracting hot air as well. That is why I am going to position a 120mm fan in the bottom 3x5.25" bays blowing cool air over the NB area to see if it makes any difference to system temps.
To be honest, I don't think this case will cool better then my Mirage or the TJ09. In fact the last time I had a Lian Li that did not use the traditional cooling (V1000 - not the plus model mind), I actually found the PC7 superior. I think the traditional 1 fan in, 1 fan out, and maybe a fan to cool an sli setup works best. Lian Li have been setting up their cooling differently in the last few high end cases (just look at the G70) and I don't like it as it means arsing around with fans, heatsinks and whatnot.