Most of the time playing on a (steel string) acoustic is a very good thing in my opinion. Just because it is harder to press down the strings and do certain things you really build up more finger strength in comparison with an electric. After that, doing the same song on an electric should be easier for your fingers.
But no, your tone has really nothing to do with learning the song. As long as you play the song correctly on your electric if you play it live then there's nothing to be upset about right?
JJ