I don't think you're being unreasonable either. But, you also have to be realistic about the situation. They are going to have to touch, pry, move, and stow many trim panels from your truck. Your seats may need to come out so they have room to maneuver the dash.
They are going to be doing a fairly invasive repair to your truck. I know you want your truck to be perfect again. And I know they should be able to give that to you. But, there is a very real possibility that there will be new (albeit small) imperfections. I don't expect the major issues some mentioned like squeaks and rattles or things not fitting right. But, I don't expect it to be 100% either.
Trust me. I know exactly where you're coming from. I bought a $57k 300 SRT back in 2014. My brand new car had barely 1k miles on it when I discovered that the spoiler is designed in such a way that when it gets hot, it expands and rubs the paint off the trunk. My beautiful car had two bare metal spots next to the spoiler every time it wasn't in the sun. I was sick to my stomach and couldn't even look at it for a week. I could have had it repaired, but it's a repair - not an undo. They were going to need to re-paint the entire trunk lid and blend into the quarter panels because it's a pearl coat. Nobody could guarantee me that it would be perfect because of the size of the area and the way the pearl lays. All I wanted was my car to be back to the way it was, but I knew that it would never be exactly the same ever again unless I found a time machine. It's unfair and maddening and frustrating and a whole bunch of adjectives. I've learned to live with it now but it still gets to me.
I sincerely wish you the best and hope everything works out. Just make sure that you've really thought about the situation, your options, and have considered the outcomes other than the ideal one. Only you can make the decision of what's right for you and for your truck.