The manual should be much clearer about the "VGA Ventilation Duct." The poorly-done manual (what a piece of crap for a $150 item) says nothing about installing the fan. This duct, of course, is made from two halves that can be taken apart. There is and 80x80 indentation in the side of the duct facing the PCI cards, and it looks exactly like it's supposed to contain the fan. Intuition would certainly tell you that you put your fan in there and then insert the screws from the inside of the duct. When I did that, there was not enough clearance between the protruding fan and the heat pipes atop my passively cooled Giga-byte Radeon X800XL. It then dawned on me that there's room to mount the fan totally inside the duct. I placed it there, inserting the screws from the outside of the duct. That left the Antec TriCool's control switch on the inside of the duct where it can't easily be adjusted, but that's OK -- I set it to Low and forgot about it. The fan's noiseless on this setting but produces a very good air flow. In this configuration, there's room for the duct even with cards that have heatsinks or heatpipes protruding above their top surface. (I used a Vantec noise-dampening kit to mount the fan.)
You're correct that the manual is pretty weak. What were they thinking to do the extra design and build work to make a very tightly constructed case, then practically ignore the documentation? Anyway...
If you can get your hands on an Evercool or Zalman 80x80x15 fan, it will mount properly on the duct and only add about 2mm outside of the housing. Mounting a fan completely inside the duct housing only gives it a slim area to pull air in across the fan blades. Shouldn't exactly destroy the air flow, supposing you aren't trying to run the fan at 5000rpm, but might weaken it some.
To answer sanxuau, I never really considered the SPCR version of the case. All black isn't as sharp looking to me.