hi aishwarya 

yes it is acceptable . you can give jee mains exams whether you are a private school student or nios ,and can be selectd in any of the nits as per your jee mains rank. you will be treated same as other candidates but i have heard(not confirmed) that a nios candidate have to give the jee mains exam only in some of the nios centres but this is not a big deal

best wishes