I beleive they just like to keep their areas as "clean" as possible. My maroon burrowed and under-the-rock short cut to her anemone. The anemone isn't really close to the sand either. Your tomato is just acclimating itself to its surroundings. You can say its like us humans decorating our homes or furishing it
Or you can just come to the conclusion that all clown fish are neurotic and let them dig where they please (you won't win). Also you must realize it is their home they are digging in. Not yours. :lol:
Im bettin on the Clown if she stays in your reef. You gotta let her fix up the way she likes. Move the corals or move the fish, thats about the only solution.