The airline that sells the ticket sets the baggage allowances for each leg regardless of who operates it. If you go to your receipt for your ticket, it should specify what these allowances are by leg. They may or may not correspond to what the standard allowance might be for a one-off flight on a particular leg sold by the operating carrier.
This is my understanding of IATA regulations. Of course the outsourced check-in agent at the airport may not understand that. You should bring a copy of your receipt with you to show to the agent if there is any dispute. If the agent still claims you need to pay an extra charge that your receipt says you do not owe, your only recourse may be to pay it, get a receipt from the check-in agent, and submit it to the ticketing airline to seek reimbursement.