I use a concrete drill and either epoxy bolts/screws or anchor bolts to attach pressure treated wood, or strips of plastic wood deck to the boulders a bit above water line. You can also use thin (1/8-1/4") plastic plant bed border and us several layers. Easier to bend.
I lay the layer, fill with water to make sure the liner is settled, and then use lathe screws to attach the liner down vertically into the top of the wood. There's no pressure, or at least shouldn't be, pulling down on the liner so the screws are just to keep the liner from flopping over. This also means the wood doesn't have to be continuous, so you can use short pieces.
Just epoxying wood to the rock is problematic because stuff can grow between the rock and epoxy making it weak. Bolts will hold even if the epoxy loses adhesion.
To hide... I mortar rock into the bottom of the pond and up the sides. The rock can go above the water line but for this type of application
I generally make fake rock at the top. Just easier to get something that looks like the boulder and doesn't bump out too much.
You can make rock that just hangs on the wood/liner but imo for this type of application it's difficult and could fail. Rocking the entire bottom and up the side provides a foundation for the top cap.
I would strongly recommend not using any rubberized liquid product although I know these types of things are right up there with duct tape as a cure all for most DIYers. Rubberized products require an extremely stable subsurface and even then they can be trouble. Painting this stuff on the boulder, sure, great, very stable. Things go south when the rubber has bridge from the rock to what? Liner, over dirt? Doesn't work.