Is Anna University's counselling different for CBSE and matriculating students?

No, the counselling procedure is the same for both CBSE and matriculating students. You will be counseled in the batches as per your cut off. But the cutoff calculation procedure is different for CBSE and matriculating students.

For State Board students Cut off= (math/2) + (phy/4)+(chem/4)

For CBSE students Cut off= (math) +(phy/2)+(chem/2)

Apart from this CBSE students get normalisation as it’s difficult to get such high cut offs. Under this, usually 5 marks are added to your cutoff.