Yes, the body does generate the melanin over time. Unfortunately, when the clothing covers the skin, the melanin that generates the pigmentation to match the surround is much, much, much slower. This can be observed by performing the same experimentation on your skin that's likely to expose to the UV spectrums, such as your arm. Say you have an abrasion, your skin healed, but you cover it with clothing that will not allow UV spectrums to cause the pigmentation to occur due the darkening of the melanin, the healed area will take quite a bit of time to reach the same coloration as every other part of the exposed skin.
Yes, it will take a bit more time. Where the sun don't shine, it will take a bit longer. As long as pains and anomalies, beside skin bleaching, does not occur, be patient and continue on with your own quest for skin lightening from hyperpigmentation for the rest of the penis.
Hahahaha. Welcome to the complexity of the biological world my brother.
I wish more brothers chime in with every little issue they have. They don't believe that small issues worth the reporting, but in fact, it helps quite a bit in revealing the complexity of strangeness during PE.