Are you talking about the fan for the VRM/RAM modules? It doesn't generate that much heat (compared to the fan on the radiator), though it is a bit louder then the radiator fan. As long as you give it the spacing it needs, it doesn't cause any throttling (and better cooling doesn't affect performance, as you stated). You can definitely argue successfully that the 295x2 is trying to hit the market segment that wants the high performance but isn't willing to have a high maintenance rig (custom watercooling). I think it is successful in that target (at it's current 1k price point, at least).
You'll have bigger issues going to dual 295x2's (quadfire) then where to mount your radiators. a 295x2 requires more then 8x PCIe 3.0 speed (so basically it needs a full speed 16x PCIe 3.0 slot) as well as 50 amps on your 12v rail (or 28a per rail if multi-railing). Going to two of them means you have to go to an enthusiast chipset like the x99, with at least 32 lanes of PCIe 3.0 (16x\16x) and the motherboard has to have the 16x slots far enough apart to allow for the cooling with the onboard fan, as well as 4x 28a rails (or 100a single rail for GPU's alone) and a 1000w+ (quality) PSU. The requirements for 2 295x2's is higher then 4x 290x cards (but requires less slots)
If you already have a watercooling setup, you'd be better just buying individual 290x GPU's and scaling up to something like Trifire 290x (performance drops off a lot from 3 GPU's to 4). Some of them come with waterblocks already installed, even.
I'm not familiar with the chip you're talking about but it sounds like a thermoelectric cooler (like a peltier?). The problem with those is if you have any humidity in the case (and you would), you'll get condensation on the colder then ambient temp components.