Can't change RGBA shader values in animation clip when I set them to legacy?

I've made a number of animation clips using the native Animation workflow and in particular had a number of objects fading out during the animation while others remained visible by varying the alpha value. This all worked fine until I was told I had to change the clips to legacy in order to call them in script using animation.Play(). Now that they are in legacy there is no fading effect and the RGBS values in the Animation window are greyed out. The script can't find the animation clips if I keep them in type 2 rather than legacy, type 1.

I've read a lot about how this change came about in unity 4.3 or so but can't understand definitively if what I'm trying to do can't be done or if there's something I'm missing?