I've just filed an RTI application with MEA, Govt of India. They have to reply within 30 days. Let's see what they say.

There is a notice on the Passportindia website about how the GEP verification is carried out on behalf of the US Government, and therefore is not subject to an enquiry under the RTI Act. That is incorrect as the GEP verification is carried out against an application made by an Indian Citizen and on payment of a ₹ 500 fee. If they had not charged a fee, they might have had a case, but GoI does nothing without charging fees!

If any of you would also like to file RTI applications, it is pretty effortless to do so. Go to the rtionline.gov.in website, register and then file a request to Ministry of External Affairs, CPV Division. There is a fee of ₹ 10 payable, which can be paid by credit card. I used an Indian credit card. In my application I mentioned that I had paid a fee of ₹ 500 for GEP verification and therefore was entitled to make an enquiry under the RTI Act. Once I hear back from them, I plan to file additional RTI requests to MoF and MHA if that is where my clearance is pending.