Really, the only reason why fan noise is ever a problem is because GPUs got the short end of the stick with ATX form factor - two or three expansion slots doesn't really give enough volume or cross-sectional area to hold the kind of heatsink and quiet fan that CPUs get. Since high-end GPUs are 250+ watts and high-end CPUs are only 130W, we ought to be giving the GPUs the wind-tunnel treatment and use the smaller down-blowing fans on the CPU.
Well, to be fair, when ATX first came out video cards didn't require two or three slots. Most of them were single cards with passive heatsinks. I don't recall video cards having fans at the time but it's possible.
Actually, if you bought a Voodoo then you needed two slots; three if you did SLI.
The setup you describe is done now, more or less. My case has the video card at the bottom directly in front of a large fan that blows outside air across it. The card itself has two fans that suck that air in and partially blows it out the back. At the top the CPU has a small attached fan with a large fan on the upper rear of the case sucking hot air out. Some cases also have an extra fan on the side of the case directly above the CPU.
The only thing missing is the tunnel as you describe. But I have seen people do that with custom SLI rigs. I think that the problem isn't necessarily the ATX form factor, meaning the motherboard, but the case design itself. I've seen some creative case designs from pre-built computer manufacturers but it makes it difficult to service yourself.
