Rough air is a funny old thing. I've followed people through passes who have been reporting turbulence which was going to shake their engine off, and I encounter what I describe as light occasional moderate. Sometimes I hardly feel a thing, the bumps have gone elsewhere. The vast vast majority of turbulence in the UK in VMC will be light, severe turbulence means uncontrollable plane and (on the very very rare occasion you hit it in the flatlands) will last seconds. True moderate turbulence can be quite unpleasant and yet most people think they are going to die and report it as severe/extreme.
Now I agree that all bets are off in the mountains, and I've been woken up in the back of a 747 when crossing the Alps. However for every person who finds it smoother in the valleys I will find you another who find it smoother several thousand feet over the top. Sometimes I am tightening my belts as the previous five times I have gone over a certain ridge I have nearly lost my teeth, and it is as smooth as silk.
As I said, when flying around the mountains you need options. Being 5,000 feet above the highest mountain gives you more options than being in a valley 2000 feet below the peak. If your plane can reach FL200, you are licenced to be up there, and you have O2 then I will take FL200 every time.
You might still get shaken around, but that's the price you pay for being around mountains. Mountains have local weather systems which are essentially unforecastable, and winds aloft will be wrong in places. That's why you have to pick your comfort level. If winds are forecast at 30knts at the level you are crossing then you can bet the mountains are somewhere producing winds doing 60knts. It gets bumpy, such is life, and if the forecast winds aloft aren't all over the place I'd go over the top...