EOS 600D use DIGIC 4 while EOS 650D use DIGIC 5. Does this produce different raw file? That is, is data collected from the sensor processed by the DIGIC X before saving?
The RAW files are different because the sensors are different. The processor does not do anything to the RAW data, it simply reads it and packages it in a RAW format. The embedded JPEG preview though is computed differently by these processors, just like a JPEG would.
In theory, yes, the phase-detect pixels affect image-quality but the effect is extremely small and it depends how they are masked. Each phase-detection pixel is very similar to having a hot or dead pixel. After all, it is either masked completely from the output data or gives a different signal due to the microlens needed for on-sensor phase-detection.