So, is this CO law in conflict with the Firearm Owners' Protection Act (FOPA)? "One of the law's provisions was that persons traveling from one place to another cannot be incarcerated for a firearms offense in a state that has strict gun control laws if the traveler is just passing through (short stops for food and gas), provided that the firearms and ammunition are not immediately accessible, that the firearms are unloaded and, in the case of a vehicle without a compartment separate from the driver’s compartment, the firearms are located in a locked container"
FOPA doesn't cover mags, just guns.
However, if you have a couple mags secured along with the gun they go in and are only passing through the state as required I doubt you'd get any trouble in CO. I wouldn't want to test it driving through NY as they don't seem to honor even the firearm portion of that law.