The Planck units can be used for anything for which other unit systems can be used. That is not as much a question of physical accuracy, but rather of mathematical notation convenience and derivation error avoidance.
When investigating microscopic quantum systems, it is often not necessary to be reminded all the time that the permittivity is in principle part of a formula, it just enhances the required amount of writing. On the other hand, when you go to the macroscopic world, using a unit system in which the permittivity is "spelled out" is a good idea because you are less likely to forget that you e.g. need to correct from vacuum permittivity to glass permittivity.