Tiling Over Drywall Problem Help Please

I am finishing a remodel and the tile guy doing the installation, applied all of the stone in the bathrooms, and kitchen to drywall (greenboard in most areas) but some areas were regular 5/8" wallboard, with thinkset and a latex ad mixture. All drywall surfaces had been skimcoated with topping mix and that is what he went on top of. The showers did have cement float and the countertops did have a hardibacker underlayment. He ran silicone along the connection where the countertops meet the wall. I had thought it was waterproofed and he told me that that was not necessary with the Laticrete Ad Mixture. I have come to find that this may not be true. I cannot rip all of the work out now, it is extensive. What do I do? Is there something that I can seal the stone and grout lines with that will essentially prevent moisture or water from getting through? Any help or advice would be appreciated. Should the drywall have been cut out in the areas where the stone was to go and wonderboard or floated cement inserted instead or is it normal to go on top of drywall???
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My preference, if water can even remotely be a possibility, is to use Durock. Hardiboard is, in my opinion a second rate solution.
Now that you have tile and stone over greenboard (ugh!) and gypsum just be sure that no water gets through to the substrate. I'd apply sealers to the grout on a periodic basis (at least once each year) and if water will stand at the intersection between a wall and counter surface caulk well. My preference is polyurethane rather than silicone, but either is better than nothing.
Your "tile guy" took too many short cuts. They may have improved his bottom line but you paid for it.
RB
Michael Roback wrote:

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