Never seen it done, but I guess it's theoretically possible. You'd need to pull the plastic liner to install the rivnuts in the factory holes and then reinstall the liner. Next, you would have to attempt drilling through the plastic bedliner in all the right places to line up the bolts for attaching the rails.
You may also need longer bolts to account for the thickness of the plastic bedliner. TBH, it will probably be easier (but not cheaper) to ditch it and get a spray-in.
I ditched my plastic bedliner and someday may add the rails, but do not have an urgent need.