A rule for adverbs in the Active Voice is to place the adverb after the (first) auxiliary verb. The rules for placement of adverbs are less restrictive in the Passive Voice.
Take the sentence:
"She sang beautifully."
The adverb MUST come after the verb. We cannot say, "She beautifully sang."
In the Passive Voice, we can say:
"It was sung beautifully."
AND
"It was beautifully sung."
Let’s look at your sentence in the Active Voice:
“The author uses the two words interchangeably throughout the book.”
And
“The author has used the two words interchangeably throughout the book.”
The rule is, ‘after the auxiliary’; yet to say:
“The author has interchangeably used the two words interchangeably throughout the book.”
…sounds most odd.
Similarly in the Passive Voice:
“The two words have been used interchangeably throughout the book.”
Again, to say, “…has interchangeably been used…” would sound odd, as does:
"…are interchangeably used…"
My sense is that it is not so much, "The two words are…"WHAT```````````? "…interchangeably used."
and more
"The two words are used…"HOW?"…interchangeably."
It appears the caveat that grammarians state when it comes to adverb placement, “there are exceptions to the rule”, applies here. Said grammarians don’t mention, from their collective experience, just what all the exceptions are, and it is left to us to stumble upon them. 