Both the Japanese and Soviets built DC-3 variants under license and these are allowed as skin substitutes by HTC. What is and isn't allowed as a variant for skinning is a complicated issue and if there is any likelihood of a skin being rejected I'll always ask HTC before starting it.
My take on the captured aircraft and assembly ships not being allowed is this: Such an aircraft was not being used in RL for the same purpose as it will be used in the game, i.e a combat aircraft. Assembly ships were old retired airframes stripped of armour and guns and painted up brightly as a focus for formations to form up on. Once the formation was ready to head for its target the assembly aircraft turned back to base before getting anywhere near the enemy. Captured aircraft were used for testing or training but not for combat.
The Japanese P-40s that were used for combat are an interesting case. Has anyone asked HTC about them? I guess it would depend if it was a long term use at squadron level or just a handful of sorties. Possibly HTC would just kill it to avoid "If we can have a Japanese P-40 why not a......" all the time.