To answer your question as to why a production model could not get a custom color : because it would no longer be production.
Production line is designed to make instruments according to specification, so that they can create them more efficiently, and cut the cost of the instrument by using time changing colors and such. I know you would be willing to spend 3-400 dollars extra, but you gotta understand that a company with the size of Gibson, has a production line that turns out a significant amount of guitars. To have to stop, deal with lists of custom color options within their production line would seriously reduce their productivity, as well as have to create a totally new division of personnel who's job would be to take orders, and make sure that these guitars are sent out to the right people. Also, if they start doing that, what stops people from saying, ''All I want is a regular production Les Paul, but with an ebony board'', or 'different inlays'', or '' a different kind of wood for top''. These are all one change to the guitar, and individually don't represent a big difference, but on a large scale operation like Gibson, it kills your production method.
So, to solve this problem, they create a custom shop. The custom shop doesn't work like production, because it's not a production line system. It's where guitars are made according to a unique customer's specifications. Be it a different color, a different neck profile, a different wood, etc.... they will make it. Now, because they vary so much in specs, they have to hire their best guys in this division, the skilled A-listers. They also have a whole team to help you get your specs in, and get you the guitar. The reason why they can't grab a guitar of production and spray it for you, is that this would overlap both deparments, which would create problems as previously mentioned. Their job is to build instruments who do not fit in the production line. Because of this, even for a minor difference, you have to go through their process, not the production line's process, to get the guitar. This will mean a cost that is significantly higher because a) they don't operate in the same way, and b) they are a custom shop, so the instruments they turn out are held to a higher standard, which they want to maintain, instead of grabbing production guitars and stamping they CS logo on the back of the headstock, which would lower this standard.
It's a mix of logistics, and a system that tries to keep the production line flowing, while allowing people to be picky about things like color, inlays, or special woods, if they choose to spend the extra. They are not doing it to be a pain in the neck, it's just not a viable option for any shop.
Hopefully this helps answer your question.
Edit : PS. For non, standard colors, they have been known to offer color variation in limited runs in the past, like different shades of blue, orange or red. They evaluate this on a basis of what is requested most through surveys, and through the custom shop.
