I think it depends a lot on your UI type/style and how many separate images you want to have in your atlas =)
Me personally, i prefer to have as few images in the atlas as possible so the atlas image is as small as possible in most projects.
For many things one can create all sorts of shapes by just having a few base shape images in the atlas and combining them to different other stuff.
Adding support for gradient sprites would enhance that flexibility a lot.
As you said it, right now one would have to have one image for each gradient if one goes the way of storing the gradient in the atlas, and yeah, that's not just not ideal when for some things one wants to have many gradient combinations be possible but also when one wants to change the gradients' setup at runtime.