Does camera clarity vary with to the app?
Yes, software tweaks have a massive effect on image quality, and the htc sense version was optimised for you sensor, whereas the cm app wasn't, this is the difference between a well optimised app written to play to the strengths of a specific platform, and a general app written to give a moderately good experience on average. This same thing can be applied to cm more generally, with apps that use specific hardware (e.g. dialer) often having a worse experience compared to stock.