Hi Jeremy,
I don't think that there is anything "wrong" with the guitar, per se, It's just that given how that particular guitar "came out," the neck had to be shimmed up at the end to get the proper geometry for proper action. That it plays as it should and sounds good is testament to that.
OK, that said, it is completely unacceptable to me. That is an aesthetic boondoggle that is completely out of line with the price of a GSm, as well as the reputation for Taylor quality. Sorry, but that this one guitar sounded better than the other GSms in the store says nothing to me, personally. One may vary slightly from another, to be sure, but one GSm is not going to magically sound amazing putting all the others to shame. It's a "simple guitar" ...nothing fancy or exotic about the GSm; just a solid, competant guitar at that price strata. So would anyone here accept this neck join from any other manufacturer at this price??!! No reason on the planet that a proper GSm shouldn't have good tone, good action, and good aesthetics. Up to you, of course, but that is not what I'd be comfortable with paying 4bills for. Hope that doesn't sound harsh to you. But it is how I feel considering this is no cheapie hun-dollar import. I'd personally seek a solution that is comensurate to the cost of the guitar.
Edward