There is no 2-piece allowance on domestic flights unless booked as a single trip combined with a qualifying international flight. Now sometimes the rule may be waived, but it depends on the agent and on the phase of the moon rather than on the airline.
I have had luggage fees waived by Jet, Deccan and Kingfisher after stopovers, even though the 2-piece allowance only applies to connections. I've never tried to do this with separate tickets, and even if I had, my experience would not translate to a general rule.