They did do something different. The current Apple TV dual core with one core disabled A5 is 32nm. The fully functional A5 in the ipad 2 16 2012 model is a fully functional A5 also at 32nm. So at 32nm, which is about half the size of the 45nm A5X of the ipad 3. Half the heat, or less than half.
I see no reason why a 32nm A5x which sports a dual core A9 and Quad core GPU couldn't fit in a iphone 5. But your are correct even at 32nm, it may still be too hot. A Quad core GPU gives off more heat than a dual core GPU or a Quad core CPU.
With some OS and speed tweaks it is possible if the iphone 5 is slightly bigger with a bigger screen. A good GPU is more important to IOS devices because IOS 5 uses hardware acceleration at more than three times the rate of Android devices which are not running 4.0 yet or ICS. ICS takes greater advantage of hardware acceleration and does a good job at it. Not at the level of IOS 5 yet, but close. ICS is really impressive to say the least. Biggest update to Android to date.
Tegra 3 fits in a phone just fine and that is 40nm. But is a quad CPU not GPU. Exynos 4412 is also a Quad CPU and not GPU at 32nm. The A5X is reverse of the those two, dual CPU and Quad GPU and curently 45nm which has something to do with the excessive heat. At 32nm it would not get that hot.
We may also see the first A15 Cortex SOC with the A6. The Snapdragon S4 is a custom design which uses the Cortex A15 reference designs, but is pretty much a in house custom designed SOC. Qualcomm licences the reference designs only, thats it.
Whereas chip designers like Samsung and Texas Instruments (TI) license the architecture for ARM’s Cortex cores. Companies can also obtain an ARM architectural license for designing their own, different CPU cores using the ARM instruction set. Qualcomm designed their own ARM-compatible cores based on the reference designs only and custom make the chip.
The Snapdragon S3 was based on the Cortex A8 and A9 reference designs. Not just the A8 as most believe. Reference designs are allowed to be used even before ARM licences out the architecture because there are not many SOC's manufactures out there that can do much with just a reference design. Qualcomm is one of them. I know ARM is worried that Qualcomm will start to use there own reference designs, and that may be the case with the Snapdragon S5 which may or may not be based on ARM. The cortex A15 and the Snapdragon S4 both are about 30 to 40 percent faster clock for clock and core for core than a Cortex A9. Both scale to 2.5Ghz and are also made to be used in laptops(ultrabooks) as well as tablets.
Most don't realize that the Snapdragon S4 is a more advanced design than even the Cortex A15. More efficient clock for clock and uses less power. There are not better chip designers than those who work at Qualcomm, and that is including intel. Intel only has to worry about the CPU and GPU, SOC's makers have to worry about allot more than that.
There isn't alot different design wise between a Cortex A8 and A9 arm chip aside from scaleability. Now there is alot of difference between a Cortex A15 and a Cortex A8 or A9. Same as there is a big difference between a Snapdragon S4 and Cortex A8 or A9.
A small point that doesn't affect your claims. The Mali 400 in the Exynos 4412 is a quad core. In terms of GPUs, cores don't really mean much as each core can have varying processing capability. Some cores are smaller, some are bigger. I think the Power VR 543MP4 is a much larger than the Mali 400 but I don't have the numbers to back me up. Regardless, heat comes down to a lot of things like the build process, clockspeed, size, etc.