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you can't paint with white...
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I'm going to make a blanket statement here. Paint programs will handle alpha channels in different ways so YMMV...
True IF you declare 255,255,255 as the color of your alpha. Change your flag background color to 255,255,254 (or similar) and you should be able paint. The user won't notice the difference...
I've been adding and merging layers in my tests on the new vessels for exactly the same purpose... adding 2D details to keep the poly counts down...