If I were to customize and order an AR (complete) from ST, and request a class 3 barrel length, would I be able to just pay the $200 tax stamp and form 1, instead of jumping through hoops for "manufacturing a sbr" (pairing a short upper on a rifle lower) because you guys (spikes) sent it to me assembeled? I'm not clear on how exactly this works.

Please look at the NFA section of the forums. There is an existing thread on this. If you wanted a factory SBR there would be at least an additional 200$ cost to the weapon for them to make it on a Form 1. It would then be transferred to you on a Form 4, which is another 200$ stamp.