In a way, yes, but don't think of it like a photoshop layer! The borders to the alpha may not behave the way you like with the [ctrl]+[s] option. However, you can save components, which will split the image into two files: one of pure colors and one with the material only, like a height map.
Check the
INFO thread!
especially this section:
[Shift]+[s] to save as...
[Ctrl]+[s] to save active layer only as 16 bit PNG with alpha
[Ctrl]+[Shift]+[s] to save image as two 16 bit PNG images of components: Color only and Material only (height image). Filename gets suffix "_col" and "_mat".