Okay lets think this through. Why do they say to cover the screw heads? They are worried the screw heads might have a bur or such on it that might puncture the liner is my thought. So your thought of putting some flex seal tape is a solid one. I would not even try to put something behind the liner at this point. With the $1000

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worth of water in it I really don't think there is any way to get anything in there.
The tape on top will protect it if/when someone leans on that part of the wall. Just like you said, a pre-patch!