The deeper you go into this world the more upset you are going to get. Basically the answer in pretty much absolutely any dispute or anything out of the ordinary is "merchant pays". It's not worth your time to dispute it in the manner you did, as you will likely find out over time.
Your story sounds like at least a dozen merchant banks I've worked with in the past in various capacities, I'm honestly surprised they even spent that much time talking to you about it. Things may be changing this day in age, but 10 years ago basically any card not present transaction that was disputed you automatically lost, and the Visa or Mastercard network would charge you the $35 for the trouble of you being defrauded by a customer :)
With one gateway after we switched providers and took the interface out of production we received about 5 fraudulant payments in the month that followed. Someone had hacked the bank's "iframe" service that we did not use and even though we only had the account open for a potential rollback we were still liable for $20 x 5 in fees. It was entirely the bank's fault.
You absolutely have the ability to not charge me a $25 fine (which appears to go to Stripe) when all of the evidence from the customer and the vendor show that it is a valid charge – and the customer has in fact told the bank to reverse the flag on the charge. What basis is there for charging a fine for something when the underlying charge has been reinstated by the customer?
Instead of a reasonable process, I got the runaround for months and bogus excuses (e.g., driver's license request). As another commenter mentions, your dispute resolution system is so poorly set up that it's not worth jumping through your hoops — just to lose at the end of the day. I am actively looking at an alternative processor because this was such a hassle.
I have another startup which has processed only 30k and had 9 disputes. I won one dispute (4 charges) but only because I got the customer to agree in writing that he would withdraw and I would refund. I submitted a screenshot of my conversation with him in Intercom. He withdrew it and I refunded him as soon as I could.
Seems like it isn't really worth the time to submit evidence unless it's for a lot of money or the customer agrees to withdraw and calls off their dispute. Def. in the customer's favor.
Stripe said we lost the dispute because we didn't provide the customer's driver's license. (What?!) We persisted and at this point contacted the customer, who readily admitted that he was still using our software and was happy to pay for it. Unfortunately, even this was not enough for Stripe, who refused to reverse their levy on us. They claimed that someone had stolen the CC from its true owner, signed up for our software, and was emailing us from a fraudulent email address.
At this point, the customer (who was really nice) called their CC company several times to say that it was all a misunderstanding and that the charge was justified. But Stripe refused to accept this as proof. They might not be as bad as PayPal, but they're not saints either.