I think you are on to something big. Not necessarily for Flipkart or PayTM though. Right now, the Google and Facebook are gatekeepers to the internet, cornering most of the ad revenues. Similarly Google and Apple are gatekeepers to the mobile world via their app stores.
If you clone Android and move away from the app store model to one where the phone only has pre-installed apps, you can potentially subsidize the hardware (and maybe even data charges) via commercial revenues. This model did not work for Kindle Fire because it was targeted at a different market. Even in India, most current active urban middle class smart phone users would hate it. But my guess is that there are hundreds of millions of people who'd happily pay Rs 500 for a smart phone plus Rs 50 a month in data charges. At scale, it would mean a subsidy of around Rs 2000 for the hardware and break-even for data. That's high CAC for the target demographic, but the commercialization and growth possibilities are endless. Basically, you are bypassing the current gatekeepers and setting up a new gate of your own.
(If this sounds vaguely familiar, that's because it is just internet.org with a twist!)