The usual policy is to challenge/dare the nitpicky customs agent out to make buck of you to make a note of it in your passport to ensure you take it home when you leave. Usually they step back at that point. If they make a note in your passport, make sure you get it endorsed back when you leave the country by the bored customs agents that sits at a desk after immigration.
BTW, FRRO do make notes like 'application received' in foreign passports when you submit your application for extension of your staying permit.
