Clearscope functions are functions that do not have an impact on the gameplay. They're math operations and simple information getters. From the wiki description of [wiki]ApplyDamageFactors[/wiki], it seems it'd be safe, since all it does is compute a value, i.e. it applies damage factors to a damage value, but it does not apply damage to the actor. If it has no undocumented side effects, it'd be fine. Could be used for things such as VATS-like previewing how much damage an attack would inflict on a target, for example.
Note that there is ApplyDamageFactor (singular) and ApplyDamageFactors (plural). The change was made to the latter (plural), while the OP is requesting to change the former (singular).