No, color dilation artifacts is what you actually also solve with the atlas padding that exists already today. The "inner padding" is no real magic, it just provides the missing space around the sprite to do proper antialiasing by adding an explicit 2px transparent border.
This is actually very easy to achieve -- it is basically an additional padding that also goes into the sprite metadata. So assume you have a 50x50 px sprite, anchor at (25,25). In the atlas, it would be placed now at e.g. a rect (2,2,52,52), but the metadata would denote it as a rect (0,0,54,54) and anchor now at (27,27). So the finally used sprite would effectively be 4px larger in width and height, now having a 2px wide transparent border all around.
All you would need to do is add the inner padding to the existing padding parameter on atlas creation, and then consider it for the sprite metadata accordingly. Implementation-wise, this should be a no-brainer, since you have already padding implemented.