Well on my bike i've got a triple, and it's impossible not to have the chain hitting the mech at all in any gear, the compromise is to have it so that it only touches in one combination that is easily avoidable. For me it only touches when i'm on the biggest sprocket on the middle ring (i.e. 42x23) which is most avoidable as i just go on the granny ring and 4th and 3rd for spinning up a big hill (32x17,19).
It only touches it very lightly and still shifts well, so i just accept it.
Also when i was setting mine up a bloke on acf told me it should go inside the notch (i.e. nearer the pivot) rather than round the outside of the notch (further away from the pivot) but the front mech was really stiff with it like that, so i put it round the outside of the notch and it shifts like a dream, even from small to middle with the chain on the biggest sprocket, which it didn't do without 'help' after it had indexed with it like he said. You'd think with more mechanical advantage and less velocity ratio it wouldn't move the cage as far, but seemingly it moves it enough.
Also be aware that some shifters actually have FOUR index positions not 3, so you can trim. e.g. mine's got 1, 2, 3 and 4 - weirdly, you can go from 1 to 2 and 2 to 3, or 1 to 3, but 3 to 1 seems one motion - it won't go from 3 to 2. 3 to 4 and 4 to 3 is fine. also 1 to 2 isn't enough movement to actually change gear.
But I only use 1, 3 and 4, as they give the best positioning of the mech.