My experience of the dealers is that they are plug ins and only want basic things that make money and so what they're told.
Most things can be done but usually it is down to cost.
You can skim anything a tiny amount but too much and that's where it can be a problem. Damage to number 4 piston shouldn't have damaged the head except the bit where the valves are which can't be skimmed or rather would make a difference as it is the bore.
Either way I think maybe that isn't why it is smoking.