In cases tile contractors have to adjust there thickness to reflect the inconsistencies of the Tile. I had a floor installed that was made of mexican clay tiles whose depth varied as much as a half inch, most times it varied within a single tile. The contractor hated doing the job but it came out looking great.
I think in your case it is a question of the skill of the contractor that is at issue. If he is recommending it he probably knows what he is doing.