Yes, if the candidate meets eligibility for both, they can apply separately. However, the processes and schedules may overlap, so careful planning is needed.
For Masters, allotment is based mainly on NIPER JEE rank and category merit. For PhD, allotment also considers research aptitude, interview performance, and availability of supervisors.
No, the counselling process differs for Masters and PhD. While both involve online registration, document verification, and seat allotment, PhD counselling additionally considers research experience, interviews, and availability of research supervisors.