I thought the reason stealth bombers were black was so they wouldn't be seen at night, but thats beside the point. I was referring more to the fact that its a drop ship, and presumably would need to drop off agents, remain in place or take of undetected, then retrieve the operatives after mission complete. So some form of optical camouflage would be necessary. Obviously if its intended only as a carrier or bomber that doesn't need to land in hostile territory its no so necessary.
If visual camouflage was necessary, and presuming the tech to use a digital camouflage (as in LED, not the pattern) isn't available to you troops, you could have a dark or light blue depending on day or night ops on the underside, with the top half and sides with urban, forest or desert camo based on the environment (these agents of yours seem special enough that they likely take on smaller amounts of highly specialist jobs, if thats the case re-paining for specific climates shouldn't be such a hardship).
I final thought would be if the ship is going to be landed then remain in place until extraction, some camo netting fixed to motorized winches to the top sides of the craft could be useful. I see it as a easy to deploy visual camo that can be winched back quickly in the need for a 'hastey' lift off. If the level of technology is there this netting could be sheets of fabric that could help reduce things like heat signatures from showing.
Anyway, just a thought. Your stuff always makes me think too much XD