i don't know. doesn't the Custom Shop function separately from the Gibson USA shop? i.e. this is still a hand crafted instrument, and the extra attention and labor accounts for something. My son plays flute in his HS band, and I bought him a Yamaha "intermediate" flute after comparing them to the "professional" ones: the price difference was staggering (~$1300 vs ~$2500, being essentially the same materially).
this all said, we vote with our wallets: maybe someone's dream instrument is a custom shop special in red... :)