In the 80's we put every frame on a surface plate before we built the bike up. Most needed a bit of bending, the frames were all steel so could be easily aligned, and we had a surface plate. I don't disagree with any of this manufacturing and warranty talk but it says that alignment is hi-tech, difficult, or not important to mtnbikes (at least, not to be expected on a mere $2000 frame). 

Without a surface plate reference it's hard to know what's wrong, but alignment is NOT difficult to check. There's a YT video about the Jackson brothers, English frame builders, that shows them holding frames up to window light to check alignments.  You can run a string from dropout around the headtube to dropout.  The 2 wheel rims in the frame should touch a straight edge at 4 points.  And the bike should ride straight ahead on its own. Many of the above comments show riders do just fine at discerning misalignment.