There is no individual subject wise pass marks for JEE Main so its fine if you have 58 in Chemistry. The aggregate is checked for admission purposes. Mind you this top 20 percentile generally is much in use when it comes to home state quota of NITs. For the All India and other state quota seats, there are plenty of candidates with more than 75% in their class 12 though the eligibility says top 20 percentile or 75%. However, my advice would be to fill as many choices as you can so you dont lose a seat.