I understand your concerns, joden, but the Custom Shop has turned out to be more of an advantage than a pain for me.
After playing with the discount bundle for a while, I decided to pony up for the Total Studio 3 bundle (at half normal price). Because of the overall size, I ordered the boxed version, so it will be a few days before it arrives and I can report on all that kit. At least, it will allow me to take advantage of the Jimi Hendrix Anniversary bundle for another $40 to add to Amplitude 3, which should easily round out my guitar tone-shaping ability.
Thanks again, DigitalBoston for the heads-up with the OP!
Joel