Yes but there is no need and it will make blending the two harder.
The reason you would get transparency by applying something to your colour is because you must have an alpha channel in your texture, maya is assuming you want to use this as a transparency map and automatically linking the alpha to trans.
You can correct this by using the connection editor.
In terms of making your moss not shiny you simply need to add a specular color map which is one colour to describe the spec of the main body and then paint the areas where the dirt / moss is black.
Specular is a multiplier for your reflectivity too, so if your reflectivity for the main body is 0.5 meaning half but your specular is 0 you will get 0.5 * 0 = 0 reflectivity.
Do some tests throwing some fractals on a sphere then drag around the gain to see what effect the attributes have.
FX supervisor - double negative