Indian Institute of Technology, IIT Bombay

Firstly, you have to give JEE advanced to get an admission in any of the IIT

Don't compare them on the basis of the package. Do whatever you really want to, else after joining wrong course will make you regret whole life. Although I will suggest to for IIM whatever you get, rest is your choice.

You will have to contact the authorities for this. And in these cases the decision of the authorities is final it may or may not turn into your favour. You can only raise your issue but can hardly do anything about it. Good luck.

JEE Mains scores matter for qualifying eligibility for JEE Advance.
Admission into IIT ( Mumbai) is based on the scores achieved in JEE Advance.
JEE Mains score also matter for seeking admission in NITs & some engineering colleges.

The admission in both (IIST& IIT) are based on ranks obtained in JEE Advanced (Conducted among the JEE Main qualifiers). Candidates who are desirous to join the Undergraduate and Dual Degree Programmes offered by IIST are required to apply separately to IIST through the online application portal (http://admission.iist.ac.in) and complete the registration and fee payment process. Further both IIST and IIT-B are premier institution of National importance, Hence no comparison can be made.

In the revised examination, to be eligible for the main examination, candidates in the general category had to score at least 60% aggregate marks in the 12th grade examinations organized by various educational boards of India, while candidates belonging to Scheduled Caste (SC), Scheduled Tribe (ST). .

To get admission in any IIT, you need to qualify JEE advanced. If you have qualified JEE Mains, you can write JEE Advanced, but you need to qualify that with a great score (rank) to get IIT Bombay, as it is one of the top IITs.

12th exam marks is one of the eligibility conditions to get admission through JEE exams. You can't get admission in IITs unless you clear the exam with good rank.