There won’t be any problem if someone gets admission after passing from the PTU counseling. This happens to almost every student. 

If you want to take admission via the counseling round then there is a concession for 1000 rupees on admission in PTU.

Compare both the institutes, if it is a government college you can opt for a refund. However, in the case of private colleges, it is your choice to get admitted. 

Before choosing, look over the stats of both the institutes and figure out the better one. Choose the college based on Faculty, academics, recognitions, placements stats. Choose the better college out of the two.