Why are you considering a liner? The trough shouldn't need a layer of small stones at the bottom ca help with draining.

What is he planning to plant? Alpines eg will need sharper drainage than other plants. And what is the trough made of - wood will need lining but the liner will need holes cut in the base for drainage. Stone or concrete shouldn't need lining unless you want to grow acid lovers, which can be affected by lime from the concrete, surprisingly. Can't see the point of putting stones underneath a liner though.