The SDF-1 has always had an air of mystery about it, it's strange origins, how the fold boosters disappeared on the first flight.
My theory is that they returend and some strange fold dislocation happened to the Macross on Macross city causing the SDF-1 to fold itself across the Galaxy. Possibly driven by the clandestine forces behind everything including some proto-culture elements with NUNs and whatever power those crystals have.
Oh yeah, like everybody predicted, this is the time for Alto and Ranka to get together as typical of Macross (Minmey and Hikaru trapped in SDF-1 interior, Hikaru then trapped with Misa as POWs in the TV series, Hikaru and Misa trapped on protoculture ruins of earth in DYRL).