This is not a bug. You have to turn off team colour when exporting to G3D, otherwise transparency in the texture is converted to team colour. See here
The reason the model views correctly in-game is because tileset objects cannot have team colour, so the game understands it should be transparent, even if the model was exported incorrectly. The G3D viewer, however, has no idea what a model is used for, so displays what it's told to. Were you to use this model in a faction, you'd find that the team colour is displayed.
I'm marking this as invalid.