I think that they did perhaps just interpret a local goddess as being a local incarnation of sorts of Juno. When reading about Celts and Slavs I remember the Latin text saying things along the lines of "The Slavs worshipped Jupiter, whom they called Perun" or "The Celts worship Mercury, called such and such by them".
Also, an interesting link between the Italian peninsula and Asia Minor is seen in the Stele from Lemnos:
The Lemnian language was apparently spoken on Lemnos in the 6th cent. B.C., and seems to be related to Etruscan. Etruscan does not otherwise have any known relatives, and was spoken in what is modern Tuscany. It exerted a strong influence on Roman culture and the Latin language as well to some extent. Perhaps there was some sort of movement between Italy and Asia Minor that gave rise to legends about an Asian origin.
At any rate, I was told in university by one professor that the romans likely did believe to some degree that they were descended from Aeneas, which is evidenced by Livy in book one of Ab urbe condita as well. He interpreted these myths as being a way for the Romans to legitimize themselves to the Greeks in a way - to prove to them that they had an ancient and noble heritage, and weren't just newcomers to mediterranean politics.