Even with Mesa I learned in my town that you cant trust what's going on in the store....
I suspect the stores (some of them, anyway) change the tubes to make the darn things not so loud.....so they can let people turn them up a bit without breaking windows. Mine had a ECC82 in the P.I. slot when I bought it off the show room floor, which I believe is the tube that has a 20% gain factor. Still sounds good, but makes it not nearly as loud. They also had 3 different brands of tubes in the first three slots and none of them were Mesa tubes.
I'm glad your custom order sounds great. On the burn channel, try doing it the other way around......turn the gain off, then turn the master way up, then ease the gain back up ever so slightly. It will get loud almost immediately, but it wont be overdriven or distorted right away, like the first 5 or 10% of the gain knobs range. It will give you a really nice punchy rhythm sound. I'm doing this with 5751's in my slots, so mine may be more forgiving than yours if you run all 12AX7's per spec. But when I do manage to get volume out of the burn channel without distortion, it is an awesome rhythm sound that's more fun than the clean channel. I aimed for that so I could use my clean channel with pedals to get a specific lead sound.