総理大臣【そうりだいじん】はヨーロッパを訪問【ほうもん】されたくさんの国々の大統領【だいとうりょう】に会われた。
"The prime minister visited Europe and met the presidents of various countries".
され is as this to link the phrase right?
Why use "を" as if it were a normal sentence? Wouldn't it be "で" or "に" as a normal passive sentence?
Are Honorific/Courtesy sentences treated as if they were normal sentences even though they are conjugated using the passive form in the verbs?
Yes, the sentence is perfectly correct. The auxiliary (助動詞) 「れる/られる」 has four meanings: 「受け身」(passive), 「尊敬」(honorific), 「可能」(potential), and 「自発」(spontaneous). Here in your example, it is used as honorific.
総理大臣はヨーロッパを訪問されたくさんの国々の大統領に会われた。
is not the passive voice, but the honorific speech (尊敬語) of:
総理大臣はヨーロッパを訪問したくさんの国々の大統領に会った。
Which literally means:
The prime minister visited Europe and met the presidents of various countries.
