Percentile vs percentage
Percentage is your marks out of 100; percentile is the share of candidates who scored at or below you.
JEE Main reports NTA scores as percentiles so that different shifts can be compared. A 95 percentile means 95% of candidates in your session scored the same or lower. A 95% score means 95 out of 100 marks.
Board results use percentage. Universities asking for "top 20 percentile of the board" are using the percentile idea on board marks.