My Mustang got rear-ended twice and repaired twice by repair companies. But it also developed a water leak from damage the repair people couldn't find because like yours it was hidden behind carpet.
In any case, what I ended up doing was I took apart the area myself and took some silicone waterproofing stuff, loaded it into a caulking gun, and I used that to seal the leak.
What the leak was in my case was some factory seams between sheet metal had become weakened and open but like ever so slightly that a repair guy would have never noticed. I found the leak by looking for dried dirt markings that indicated the path the water took into the trunk. I followed those paths up to the seams and then went at the seams with the silicone. I never saw water back there again.
This is probably easier than writing angry letters and going for a third estimate.
If you're tying to find the leak and just can't, an option is to have someone outside the car spray it with a hose while you're inside so you can find where the water is coming in.
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