I'd stick with your original purchase. The 5400 is less complicated. The dealer is a stones throw away.
The 5400 will do everything the 6000 will do and if you can stop thinking about this in money value,
there are other values worth considering.
Some things just can't be measured with dollar signs imo. Convenience, simplicity, closer point of service, closer parts purchasing and stop in anytime mentality is just as important than a few bucks. Loyalty seems a forgotten virtue these days.
Do you think a dealer 3 hrs away will be at your beck and call should your tractor needed to be picked up?
Yes, your nearest dealer will work on the 6000 but he will always prioritize his own customers.
I wouldn't mention what another dealer is doing. You have enough info to further negotiate if you feel the need and yes, you can respectively ask for anything you want.
If money is the issue, go to your nearest Mahindra dealer and pick up the 5145 or 5155 for 7K less and just as capable.
The 55 has a turbo complicating things but has a fel capacity of 3200 lbs. Or you can buy the stick shift 4550 for 39K and still have a beast of a tractor. No cab on these however.
I feel the Kubota is a better built tractor than the Mahindra and I sell Mahindras but the Mahindra will do anything you ask of it.
The Kubota 5400 is a tried and true machine and would serve you well.
I gave you a complication to demonstrate what a pita complications are.
May you stay happy and simple.