Thanks for the input Cyberdemon 
It may be very unintuitive but I think there might be some merit to using the PSU as an intake in a case where a single large fan would be used to replace an intake fan, CPU cooling fan and PSU cooler fan. I don’t think the direction of the flow matters much.
While the PSU does dissipate some heat it actually is low when compared to the computer as a whole. A full desktop with a high end 100W CPU and mid range 150W GPU wouldn’t go much above 300W when considering other ancillary devices. Considering that it’s quite common to have 90% PSU efficiency, we expect a pretty low 30 W being dissipated at the PSU. If a 140mm fan is running at a pretty high rate, the temperature will barely rise. From some quick napkin math, I’m getting a difference of at most a couple of degrees.
It would just be to find which direction is most practical - that would really come down to the specific case the system would be designed for. However, by drawing air in through the PSU, the actual intake of air could be filtered. On the other hand, by having a negative pressure system or exhausting at the PSU, it would be hard to filter the air intake as it could be coming from basically anywhere in the case. If we’re sticking to the fact that it’s the only fan other than GPU in the case. Also, the downdraft through the CPU cooler could be used to cool the motherboard.
The more I’m looking at this problem, the issue with cooling a computer seems to be with ensuring that air is well exchanged through the case. Making sure that air doesn’t recirculate in the case. We can see this in conventional case designs where a tower cooler’s fan is very close the the computer’s exhaust. Also, in a lot of OEM workstations, ducts will be used to force certain airflow paths. I would imagine this would actually make smaller cases cooler than larger ones if the flow path is efficient.
For liquid cooling. I may have mentally dismissed too early them mostly due to the fairly large overall volume and noise. But I really should give them a second look. They do allow for a very low height clearance above the motherboard while keeping a pretty easy installation.
I need to get moving on this as we’re basically speculating on hypothetical situations at this point. Some of these choices will probably be very clear based on other factors that come into play in an overall design.