Yes, I think putting the fan in its "normal" place atop the PAL8942 may work better (with a duct) for these reasons:
1) The fan is deeper inside the case--so it generates less noise.
2) It is positioned right next to the heat source (CPU), so it should be more efficient at pumping hot air. Farther positions may be less effective due to air friction.
3) I can completely cut out the perforated-metal exhaust grille (in my case's back panel), reducing friction for outgoing air. This means I will have an 80mm round hole in the back wall of the computer, to which the duct will connect.
4) The problem of air pressure is solved, because the fan is now pumping hot air INTO the duct.
This might be better cooling-efficiency-wise, but NOT in terms of noise reduction. If the fan is attached on top of a CPU HS, it causes HS vibration, which is then transmitted to a motherboard, eventually to the case. It seems slight noise reduction achieved by 1) is more than off-set by an increase in noise due to fan-HS vibration. I have confirmed this empirically with other HSs.
You can do 3) irrespective of a fan position and that is always desirable. 4) is a moot point, to begin with, if you use right materials for the duct.
If you want to put a fan over HS, it is better to use a bracket that enables you to put a fan right next to HS without touching it, but, in this case, you have to make two ducts, one for connecting HS and a fan and the other for connecting a fan and a rear hole.