As I own both types I thank it honestly comes down to personal preference. Some custom versions can / do command a premium but not necessarily all of them
The influence of value is the model year which will put into a price bracket, this generally depreciates over time. Then a custom finish or milling will generally add value, as they would have cost more than a stock variant. Unfortunately the finish doesn't make the marker shoot better or come sprinkled with the pro player skills...
So it comes back to simple economics, supply and demand, limited runs and scarcity play a role. The personal determination to the intrinsic value of the marker is then the overriding factor, if you like and can afford it, you buy it!
Then there are some markers like the Infamous Johnny Cash SL74 Ego that were extremely sought after, which break all the rules!