Cost of assembling components in different packages
From a perspective of pure mechanics of an assembly house there is no difference whatsoever to using different package IF it is same SMD type. 

SMDs are assembled by pick-and-place machines which don’t really care about package size as long as it is size the machine can handle (going some super small packages may significantly reduce number of houses that can do assembly for you because the machine they have may not be capable of handling those sizes). In other words if the bulk of your components is in 0402, then you will be pretty safe going bigger packages for some of the components.

Things changes if you want to mix SMD and THT components as (again) some houses may not have machines capable of reliably placing THT ones and thus requiring manual work to place those. Or they may not even have wave soldering machine, which again would lead to manual soldering.