The SDF design of the SDF-1 is canon.
For the time period, anyways. The Macross is refit after the end of the TV series, and the ARMDs are attached to the location they were intended to be in the first place.
Docked with the ARMDs was the design as originally conceived(in-continuity), and as it existed post-refit.
But docking with the ARMDs at launch failed due to zentradi interference, as seen on TV. Hence the Prometheus and Daedalus still get jury-rigged on after the space fold accident.
You can't remove the Prometheus and Daedalus without removing chunks of the TV story, which is the current official story.
Besides, the official story is that DYRL is a movie created within the Macross universe, and the VFs in it are a later revision of the VF-1 that wasn't actually available during the Space War, making them wrong.
(And in that context, the Macross used would be the refit version, because the audience is familiar with that design and not the historically accurate one).