Any image with a transparent pixel, will become entirely transparent in game. Amount of pixels, transparency level, do not seem to matter.
This could not be reproduced in A2. It has been tested with same files/demo mission. Screenshots displaying the results can be found below:
Results in A2
https://dl.dropboxusercontent.com/u/39109326/screenshots/results%20in%20A2.png
Results in A3
https://dl.dropboxusercontent.com/u/39109326/screenshots/results%20in%20A3.png