You can't make trade companies on your sub continent, if you move to persia you're in Iran, so can make trade companies in India, that's why
Unless you are keeping vassals in India and use the centers to have high share and increase the goods from the vassals and the value in the nodes, I still think that strategy worse than keeping capital and full state cores in India. But it is a matter of preferences.
Despite all this, the question TS asked was how to deal with GC as Mughals. As some of you said he can spare some GC TCing India that has more Dev than Persia. Or he can simply build the GC buildings as I advised, since Mughals will be very rich.
What Ive done in my last run in the region (my 1st 1.30 run), a WC with Timur/Mughals being Confucian and Emperor of China, was keeping capital in India and TCing all the rest. The Arakan region is in Bengal node but not in India, so I made a 3rd tier TC investment for the node. The same with the Indian ocean islands that are in Coromandel node but not in India.