lol... auto engg was the plan, but couldnt do it due to some reasons 
sadly, theres hardly any way to tune a car for the best of both worlds
i.e. for cng n petrol at a time.or atleast i ve never heard of such settings.thats why tappets have to be set for cng for use on cng.
yes it is possible that they keep the clearence same... actually, theoratically, the engine should behave normally if adjusted as per the manual (even if the car is on petrol only) but there are far tooo many other factors involved.the temprature of engine when adjusting the valves n how far it is from operating temprature n soooo many other things.i remember someone on pw did his tappets as per manual and ended up screwing the tuning, so , our mechanics rely on their experience n judgement for this job...
as for ur missing, can u explain a bit more? does it stay all the time? or on lower/higher rpm or at specific speed or gears?
n theres hardly any way we can come up with a perfect reading for the valve clearence on cng ... we only have desi "jugaar" systems for cng 