If there are "shelves, typically you need to cut them in while you are putting the side tile in. I know of no good way to do this after the fact. You could certainly remove the side tile and do the install....but that's about the only way. The bottom shelf marble could be installed after the fact..but I would still remove the tile to make it look right.

I still have time to change this plan, and order a marble shelf to go in. How would this be done? The bottom tiles would be set, and then the shelf gets set on the top edge of the installed tiles. The top tiles then get cut to take into account the thickness of the stone and still keep alignment with the tiles on either side, and then they get installed. As for objecting to installing on top of the tile, yes and no. ANY kind of intrusion through the tile and waterproofing is cause for concern. But that can also be alleviated if it's "corked" back up with caulking. This one below, I'm showing you the unfinished pictures so you can see how it's done with the stone sitting on the tile's edges:

osorry1, I'm very sorry, as you are already, that this has happened to you. I run into this about every other day in San Diego, when asked questions why I have so many Sam lights compared to the other guy. One way gets you referrals, the other does not. I would look into perimeter fiber optics (rope light) that can be installed just under the coping material. They would need to remove only one piece of coping (not sure what coping material you have), cut the beam slightly, and then install on the underside of the coping product. Good Luck!

I agree with Energy Rater LA. Keep the bathroom door closed. Some people do this all the time anyway. Draw permits on any work in the future. If the bathroom remodel is discovered and the inspector insists on inspecting it at that time, fine. Respectfully do whatever you need to do at that time. If you need to pay a fine, pay; tear out work, do it. The difference between coming clean now and going in to the building department, admitting the error, and doing whatever they demand now and what I suggest above is: 1. Inspector may not see or care about the bathroom when in to inspect future work. In that case, you saved the trouble and cost of fessing up on your own. 2. If you have to tear the bathroom out in either instance, at least you are doing it later if you don't fess up. You got more "use" out of your materials and you get to replace those materials with ones that are more modern and in the "style" of at least a few years later if you wait for the inspector to find it.