I agree the sentence does seem confusing. I wouldn�t use them both like that unless making some kind of explanation.
I �m only in England for a few months. I really live in Spain, but I am actually from Canada.
The sentence would mean the same if you reversed the position.
I �m only here in England for a few months. I actually live in Spain, but really I �m from Canada.
My own preference would be to say but I �m from Canada originally. The words do have the same meaning in this sentence.
They are not always interchangeable.