The Two Towers in the title of the book do refer to Orthanc, where Saruman resides at Isengard, and to Barad-dur in Mordor where Sauron is, so your leaning is correct. The title refers to the the alliance between Saruman and Sauron.
No, that's incorrect. Tolkien intended the "Two Towers" referred to in the title of the book to be Orthanc and the Tower of Cirith Ungol, which "dominate the action" of Book III and Book IV. Tolkien also mused that the "Two Towers" might be seen to be Minas Tirith and Barad-Dur, though this was not his intention.
Peter Jackson in the film clearly intended the "Two Towers" to be those two you have mentioned.