Can I choose IIIT Bhopal instead of IIIT Vadodara as it is running in NIT Bhopal?

It may seem that IIIT Bhopal is a better option since it is being operated by MANIT Bhopal. But, try to rethink the scenario. Although IIIT Bhopal is operating from the NIT Bhopal campus, students of IIIT Bhopal do not enjoy the same privilege as the NIT students. IIIT Bhopal has different hostels, classrooms, teachers. 

Additionally, IIIT Vadodara has many advantages over IIIT Bhopal.

Placements:

IIIT Vadodara was established way earlier than IIIT Bhopal. IIIT Vadodara already had 3 placement seasons. In the three placement seasons, IIIT Vadodara had witnessed a perpetual increment in the average package, alongside the continual expansion of the placement percentage as well. 

Coding Culture:

Besides, the coding culture at IIIT Vadodara is quite good too. So, you will have major scopes for coding if you are a student there. However, the closing ranks of both the institutes somewhat do not vary a lot. But IIIT Vadodara will definitely be a better alternative. Location is the only demerit for the institute. 

A friend of mine was in the same pickle as you, a few years back. He ultimately chose IIIT Vadodara after consulting with students from both institutes. You can do the same to have a better understanding of the real scenario at the institutes.