According to what I found out from our seniors in quora, there will be no problem due to the no major system. Many of the students of IISERs go for PhD in foreign universities and also top Indian universities. PhD application form mainly depends on the essay, resume, cgpa and the references.
I hope this helps. Anyway, I guess you have not cleared the masters yet, so no need to worry. If doubt persists clear it when you get a chance to talk to any professor or alumni
Shrineel Saraf, BS-MS 2017-2022 Physics, Indian Institute of Science Education and Research, Pune
Source: Quora Digest