Is an engineer considered a "mutaffif" if he leaves cheese containers underweight (a gram or two) due to his inability to adjust the weight of all the deficient containers?

There is no blame upon you if you exert your effort to maintain the weight of the cans and the deficit in them is rare and slight, because such a deficit is often overlooked by people, in accordance with the Almighty’s saying: "Allah does not burden a soul beyond its capacity" (Verse). If you are able to write the approximate weight on the can, that would be preferable.