Most of the time I airbrush Tandy Satin Sheen on the project to seal it, then add a Fiebing's antique gel making sure to push the gel into the lifted areas to fill the voids, let it dry for a bit, then buff it to remove any excess gel. On natural colored leather, I merely pay close attention to the area when I airbrush my Satin Sheen on and spray an extra heavy coat into the . When you seal your project, the ... "raw "flesh" part of the hide you expose with the lifting is sealed also ...
If your tool is making impressions where you don't want them, perhaps try rounding the head of the tool and kicking the TOE up a bit. That way, you can cut the leather at the lift, roll the toe up and leave less visible dents to smooth.
And YES, if I want depth, I have to make it. Since leather is a 2 dimensional canvas, you create depth by beveling, stamping and otherwise making impressions into the leather. By lifting, you create a 3rd layer of depth allowing far more realism.
Hope this helps....