Well if it's the same sensor then they would have to have a significantly better JPEG engine than Sony and Samsung to produce a noticeable improvement. If they went with Foveon, at 13MP the photos would be barely usable at ISO50 on such a small sensor, not even HTC would go with that, the other option with Foveon is to limit the sensor to around 3MP, not something the marketing department would allow when Sony and Samsung are both going to be pushing 13MP. In low light Foveon is basically unusable, the most advanced Foveon with Sigma's advanced JPEG engine craps out at ISO1600, and above that it is terrible.
http://www.dpreview.com/reviews/sigmasd1/17
Compare that to the NEX-5N at ISO3200 and look at the difference. Now turn a 1.7x crop factor into a 5.4x crop factor and you can see why Foveon type sensors are just not going to be possible using current technology, and there is no way HTC have sourced some special organic dye based sensor or something like that. Their budget wouldn't allow for that and it would add hundreds of dollars to the build cost.
No, with 13MP they are using Exmor RS and trying to build it up as some unique phone camera revolution, forgetting that Sony already have Exmor RS based phones on the market and the GS4 will also use it.
The only thing I can think of is that they have developed special glass optics with a large aperture of 1.6 or lower which allows for superior performance, however, that would be pretty fragile and need a cover, not something the marketing department would allow.