1-He really is an intelligent person.
2-He is really an intelligent person.
3-He is a really intelligent person.
4-He really is intelligent.
5-He is really intelligent.
In which case:
a-"really" means "every"
and in which case
b-"really" means "in reality"
A lot depends on context and, in speech, stress and intonation.
Without these to help us, the most likely meanings, in my opinion, are:
He really is an intelligent person. The speaker is stressing the fact.
He is really an intelligent person. In reality.
He is a really intelligent person. Very.
He is an intelligent person, really. In reality.
He really is intelligent. The speaker is stressing the fact.
He is really intelligent. Very