Whiny computers are driving me nuts, so I've just started trying to achieve near silence for the first time. Components in the computer industry always seem to be out of step with each other, and such a case is annoying me right now. I looked around for people writing on this topic, but I didn't see anything specific.

I used the following, although the specific components are irrelevant, as they are pretty similar in design approach to most current mid to high end devices:

An Gigabyte EX58-UD3R motherboard
An i7 CPU
A Cooler Master Sileo 500 case and
A Thermalright U120 cooler

The best CPU cooling, whether for quietness or massive overclocking, seems to be achieved by a crossflow cooler, like I have used, in a case with a nice big fan right behind that cooler, to whisk the warm air away to the outside world.

Most high end motherboards are now laid out like the Gigabyte one I used. They have a heatpipe connecting the warm bits around the CPU (i.e. the VRM and northbridge, and sometimes the southbridge too), and heatsinks designed to cool those parts using the air flowing out from downdraught cooling of the CPU. With crossflow cooling there is practically no downdraught. The CPU is much cooler than with a downdraught cooler, but everything in the surrounding area on the motherboards goes up in temperature. Its not easy to divert some of the airflow into the required places, and adding a bunch of tower type heatpipe coolers in place of the ones the motherboard maker fits would be painful and costly. It isn't easy to find ones that will fit in the relevant spaces.

Cheap motherboards, with more elementary cooling around the CPU have less of a problem in this area. Surely the expensive heatpiped motherboards are the ones most likely to be used with a high end crossflow cooler. Things seem to be screwed up.

There is only a mismatch in relation to third-party CPU coolers. Those supplied with CPUs always seem to be of the top-down variety, so motherboard design mostly reflects that. While fitting an alternative tower cooler means that the components surrounding the CPU are not going to get the air flow intended, I am not convinced it is much of a problem. If hot-running CPUs such as the Intel i7 1366 are overclocked significantly, then it certainly can be.

I am not sure what percentage of motherboards ever get fitted with a third-party cooler, whatever the number is I suspect it is too small to influence motherboard design.

It also seems like there are a lot of new high-end top-down coolers coming out lately. Scythe Zipang 2. Thermalright AXP-140. Thermaltake BigTyp 14 Pro. So, maybe the component manufacturers aren't as out of step as the OP supposes?

Two reasonable arguments, but I think they are flawed.

Its certainly true that the hardly any low end motherboards will be matched with exotic tower coolers costing as much as the motherboard. However, those are generally not too bad for crossflow cooling, anyway. The more expensive the motherboard gets, the more likely a crossflow cooler will be used. That seems to be where the motherboards are most tuned to downdraught cooling. That seems like a mismatch to me.

Are things like the Zipang2, and AXP-140 designed to get the maximum cooling? My take was they are designed to achieve reasonable performance, while fitting in somewhat narrow/low cases, where a tower design like the Thermalright U120 won't. There is something deeply wrong about stirring the warm air around, instead of exhausting it promptly to the outside world.

Stirring warm air around case might increase some temps and not feel wise, but motherboard components, VRM's and everything immediate vicinity of the socket with top downers do benefit quite a lot the air flow they get. With tower coolers these components do not get air flow.

All motherboards are designed that they get spill over air flow from coolers. All boxed coolers are top downs and motherboards are designed for boxed coolers... Just my 2snt's... Even I am pretty biased for I am reknown top-downer...

I suppose you can argue that they are not designed to get maximum cooling of CPU, but when you factor in other motherboard components then, yes, I think they are designed for maximum cooling. It is important to understand that cooling of VRM and other MB components becomes more of an issue when you increase voltage to achieve an overclock -- which is why MB catering to that crowd come with fancy heatsinks on such components. This crowd is just as large as HTPC builders or silent enthusiasts, so it is strange to think the truly massive top-downs are not intended, at least in part, for them. You don't need something with 6 heat pipes and a 140mm fan if your goal is only reasonable cooling. Don't conflate these with coolers like the Scythe Shurikens that exist primarily to fit into certain cases. These are massive heatsinks that cater to people who are into silent computing, or heavy overclocking, or both.