A typical use case for the "clear" flag is load-modify-save, in which case most of the entity would be restored as they were. This means that any permissions checks for parts of the entity that need extra permissions but were restored (like e.g. terms) would be redundant.
In other words: permissions for modifying an entity part should only be checked if that part is effectively modified by the request. They should not be checked if the part is restored unchanged after it was first cleared.