The wise choice would be to go with your interests or the location which would be favorable for you as both these universities are really good. Still, to choose any one of them, let's have a look at the following points:

Pondicherry University:

• The university has a NIRF ranking of 87. It is well known for its campus and outstanding faculties.
• It has well-maintained and equipped labs, a highly recognized international network, and a friendly environment.

IISER Berhampur or Tirupati:

• IISER mainly focuses on quality education and for physics major students this is the most important criteria.
• They are well known for their placements and industrial exposure.

As both the universities have their own advantages and disadvantages, choosing any one of them can get quite hectic. If you are comfortable in getting into newer institutes then you can go with IISERs. But according to the alumnus, for undergraduate studies colleges do not matter that much, it depends on you individually, anyways no matter whichever College you choose they will have few drawbacks, you have to make sure that you work hard, grab opportunities and make the best out of them.