Hello Nikhil,

Well to get admission into colleges like NITs,IIITs,GFTIs one has to go through JEE Main, qualify it and then proceed for JoSAA counselling. The candidates , those who doesn't get any seats through JoSAA they then proceed for CSAB counselling through which they can get a seat in NITs,IIITs,GFTIs. Now it doesn't matter whether you get a seat through JoSAA or CSAB, in either case you have to pay the required fee since you are getting admission into NITs,IIITs or GFTIs. Ultimately these are the rules laid down by the central government and one has to follow accordingly. 

You can go through this link and checkout the details about CSAB counselling : https://engineering.careers360.com/articles/csab

Good Luck !!!!

yes, you may pay a registration fee that all college or institute take S they may know that you want to take admission in the college or institute. So if you want to stay and want to take admission they may ask for it and remain fee you may in your starting colleges time. So no need to worry.

All the best.