NIRF rankings are not the sole factor that determines an institute's worth and credibility 

Usually, rankings systems evaluate an Institute based on aspects such as international students, international faculty, and research which don’t matter much for a UG student.

Even without the JEE, IIT Bombay has always been a much more preferred IIT than Madras mainly because of its location advantage and thus excellent opportunities.

IIT Bombay is preferred because of herd mentality as most JEE toppers consider only IIT Bombay worthy of their rank. It’s like because that has been the usual trend, they have to follow it. In reality, IIT Madras has its share of toppers though the numbers might be less in comparison to IIT Bombay.