I've never made a cookie like JP, but I've done some experimenting with my RI a time or two to try and guess her technique. I've come up with something that I think she might do. Spread your flood consistency RI out on the cookie, leave it for a few minutes, and go back to it before it's completely dried (about 5 minutes). Using some icing that is thicker (say 25 to 30 seconds), insert the decorating tip just into the RI and squeeze it under the "skin". Using a thicker consistency under the "skin" lifts it up, it remains in the spot where you want it, and applying the icing under the "skin" keeps the surface smooth.
Another thing I've tried is putting piping consistency icing down and then flooding over-top it. It makes the areas with the piping icing a little higher than the rest of the flood icing. If you do this, use flood icing that's less than 20 seconds because the 20 second icing is a little too clingy for this thechnique to work.