For the top 20 percentile eligibility in JOSAA counselling, the category that is used is based on what you declare in your JEE Mains application and for which you provide a valid certificate during document verification not necessarily the one mentioned in your board exam. Since you're from Maharashtra and appeared under SEBC, you’ll be treated as a General category candidate unless you have a valid central OBC NCL certificate.

So for JOSAA, they’ll consider your category only if it’s valid under the central category list and matches what you declared in JEE Mains along with the correct certificate. The SEBC category used in the MH board won’t be considered by JOSAA unless it overlaps with central OBC NCL.