When Device Skin is set to Auto, GBC Shader is set to Subpixel, and DMG Shader is set to Dot Matrix, Game Boy games in .gb format that support color with GBC will display with the DMG skin, but will use the Subpixel shader. However, Game Boy compatible GBC games in .gbc format display with the GBC skin and Subpixel shader, as expected.
(Over a year later) Good catch - it's because the device skin uses the file extension, but the shader is chosen based on the game cartridge header. I'll look into it at some point.
When Device Skin is set to Auto, GBC Shader is set to Subpixel, and DMG Shader is set to Dot Matrix, Game Boy games in .gb format that support color with GBC will display with the DMG skin, but will use the Subpixel shader. However, Game Boy compatible GBC games in .gbc format display with the GBC skin and Subpixel shader, as expected.