Here, in the present context, 'really' and 'in fact' are about just as to what an entity (whether it be a mental entity or a material entity [that is, an entity existing in extramental reality] ) is independently of the process of knowing it. Here, we are dealing with logical entities, and they do not exist in extramental reality, so 'really' and 'in fact' do not, in this context, refer to extramental reality.
But of course, within the domain of logical entities we must distinguish between what pertains to these logical entities as such and what pertains to the intention of them. Indeed, if this distinction is not maintained (and also not the distinction between an extramental object and its intention), then we may very well be said to confuse what pertains to our mode of signifying-the-fact with what pertains to the fact itself -- and this, even though the fact in question be not a real fact in extramental reality but only a being of reason.