The surface of a flat finish has a microscopic crystalline structure that reflects the light that hits it in many directions instead of directing it back to the source or observer. Light can bounce around in the structure and make the surface look light or chalky. When the clear acrylic is applied to the surface it fills in the crystalline structure and prevents it from defracting the light. This allows the actual paint under the structure to absorb the light and it's color becomes more apparent.
The same thing happens when you clean something. Spray on a cleaner or even just get it wet and the color apearance changes until the surface dries.
Once you get your decal work or whatever completed and apply a flat coat the paint will lighten up again to some extent. It won't look like it did when you first applied the paint but it will be close.
Another place this can be seen is typically in armor. Folks have taken to mixing their own flat coat with Future and Tamiya flat base. It works well but if there is to much flat base in the mix, when the product dries it will look frosted white, not flat. This is where people usually panic and hit the boards for advice for how to fix it. A good coat of future will bring 98% of the pre-frosted appearance back and one can start fresh with a new mix of flat coat.