It’s only been a day and already I’ve uncovered the main limitation to unit icons – transparency. It looks like the sprites cannot use an alpha channel and are instead appearing as black. The game is instead trying to auto scale the images and remove the transparent pixels. This is surely a choice of the game designer and not the Unity engine, and it means means I’m going to make some sacrifices for the ability to move forward for now. However, I will probably appeal to the developer once I’ve completed an icon set to see if I can make better versions in the future.
Secondly, it looks like the unit images are located in a different location than the other graphics. I hope these images can be overridden. Otherwise, I will be creating a copy of the default unit set as well.