I agree with OP that its a very strange system. Obviously it must be effective for the airline to make money, but from a consumer standpoint it seems completely unreasonable.

I've searched numerous itineraries on Emirates and actually surprised you found the onward flight to India so much cheaper. My experience has been that you pay the same price to get to dubai and then you basically go to the next destination for free. i.e JFK to dubai is $5K but then could book JFK to Bali for ~$5.5K. Just weird