Noise is only an issue on reference cards and maybe some poorly-designed aftermarket versions (which can and does happen with any GPU).
Sure the aftermarket coolers help, because the reference cooler is ridiculous. Still isn't going to be as quiet as the 960 though which also can get aftermarket coolers. Plus the GPU cooler is just part of the battle. If the GPU is putting more heat overall into your case you have to crank up the case fans to compensate. In a hptc setting power savings get to almost double dip on the noise benefits, and there is a huge power usage gap between the 290 and the 960. Finally some of those coolers on the 290 (or the 290s themselves) can be huge and have problems fitting into HTPC-level cases. Once you hand pick a 290 based on the cooler and size you lose a lot of the relative value because you are paying full price instead of whatever is the current 290 deal.
Plus I was wrong about power consumption, it does matter for idle consumption. With a HTPC that is spending most of its time playing video or doing nothing having the lowest idle power consumption matters. From what I understand the 290 or any card based on that architecture have high idle power usage compared to current Nvidia cards overall. I could be wrong though.
I mean I agree with your overall concept that in the general gaming market the existence of the 290 proves that the 960 is a poor value for gaming. The 290 blows away the GTX 960, heck getting a used 7960 is a better value. But the HTPC gaming market is different, the priorities are different. Performance for dollar isn't the only metric.
That full HEVC decoder is huge, worth at least a $50 difference alone IMHO, while on the gaming side it has no value. Plus anything that can reduce the power usage is a huge win, it isn't like on the hardcore gaming side where power consumption can almost feel like a hypocritical talking point. We HTPC gamers weren't the ones bragging about that GTX 460 and its hogish ways, I was trying to play games on a fanless GT 450 lol. The HTPC market has always valued power consumption to have less noise, even before Nvidia made it a talking point.
As I said, it is slim pickings right now for the HTPC gamer when it should be glory days thanks to that stupid 2GB stock GTX 960 configuration. Honestly the new 4GB ASUS Strix GeForce GTX 960 is pretty much the perfect gaming HTPC card if it delivers for that reason. We get a cooler that is silent at idle, the HEVC decoding that should keep the HTPC futureproof into the 4K Blu Ray age, and the 4G of RAM needed for console ports and games a few years out. That is the card I am keeping an eye on, if it is really $210 then unless AMD just blows it out on value and power-usage in April I might get one.