On the small volume stuff the dealers really take a hit on warranty work. My bike was early on the major overhaul list at my dealer. I think it was the second one they did. It took them exactly double the time Triumph allowed for the job. Just inexperience really. They had to figure out a harness to hook the forklift to the bike to lift it off the engine. Lots of standing around scratching their heads.
Back at that time I doubt they would have run out in the street and pulled you in for a warranty problem if you had shopped the price of the bike and bought it for $100.00 less down the road. Maybe that's wrong, but it is human nature and the nature of a small business. It's hard to be generous when you are struggling. You also hear the ill advised quote of an employee who has heard the boss say, "f-this, I'm not doing another of these if they bought it from Joes Discount". But when the dust settles the dealer steps up and says "yeah, bring it in, we will be GLAD to take a look at it."
Stay cool and don't let it get adversarial.
I bought the mechanic a new Torque wrench for his struggles, especially since I rode the bike in, not thinking of the common sump, thereby allowing the bits of second gear to circulate all thru the engine. I am grateful for the effort he put in at getting all the metal out. I hope you get yours done and get it back on the road soon.