A little background information, not specific to this particular situation, is that in some states the dealers cannot collect back from Mahindra for freight charges. If the part is on the shelf already, previously ordered in as a stock order, they likely will have no freight charges. But if they had to place an order for the part to be shipped outside the normal stock order, they would have freight.
I think for all brands, the manufacturer likes to pay as little as they can deem to be reasonable on warranty repairs. It is not a profit center for a dealer, the allowable labor is really tight, and they often do not want to pay for all the shop supplies. I can understand the OEM keeping a tight lid on costs, I'd do the same if I ran the warranty department. But know that a warranty repair is a little bit of a loser for the dealer. I've heard auto repair guys say how warranty is a profit center, but we have not seen that on tractors. It is a similar deal, but the tractor world is years behind the auto world in this regard.
Having said that, this sort of issue between dealer and OEM needs to be behind the scenes and the customer should not feel it. The warranty is clear that parts and labor are covered, and it seems that associated costs like RTV, rags, brake cleaner, electricity to turn on the lights or whatever needs to be factored into the shop labor rate or recovered from Mahindra as best as possible. And perhaps in a non-freight state the dealer needs to add $100 to the initial price of the tractor and just figure he will consume that extra $100 over 5 years on freight.
California requires the OEM to pay the dealer freight on warranty claims, so that is not an issue here.
$8 in freight is a small amount to quibble over to make a customer unhappy. And $40 in brake clean and RTV is not reasonable. You can spread a lot of RTV for under $10.
I suspect the dealer is just trying to break even on the job, but that really isn't the customers problem. If it is the dealer I think it is, they are a really good dealer. I'd have a talk with the GM or owner and I bet things get resolved. Happy customers come back regularly and tell their friends good things. That has a ton of value.