in real life they started out as stencils like your talking about,but in the model world they are replicated as decals,the reason that the instruction sheets call them stencils is because they are the same markings in the same places,no matter what version or squadron you are building,they are common to the aircraft,,"no step" "lift here" "oil drain".these are some of the stencils that you may see,and thinking about it,they don't move ,so they are called stencils and separated on the decal sheet,if you were to apply them first,the rest of the decals for any squadron would still be right