See, preparatory courses are offered to those student who the IITs think that if we invest an year on these students, then these students may perform very well if they are admitted in the normal B.Tech programmes offered by the various IITs. So, if you have been selected by IIT Bombay in the preparatory course, then you'll have to do your course from IIT Bombay itself, and not IIT Gandhinagar.

Hope I have answered your question. All the best!