I thought Kawamori had planned M0 long before Lukas ever came out with all the prequel trend. It wouldn´t suprise me at all since he planned M+ years before it came out ( 1985 to be precise , from the advanced valkyrie series ).
We haven´t seen the VF-1 in M0 yet , so we don´t really know how it will look like by today standards (we just know how the VF-1 looks from 20 years ago). the only explanation within the Macross universe I could find is that the VF-1 is a mass production aircraft while the 0 is a limited release experimental aircraft (like the US and british X-35 variants).
it's actually a little more than that, not only was the VF-0 a limited produtcion aircraft, but we can already speculate that the VF-0 was never planned from the start, as it seems from what we saw until now, the VF-0 was a rushed VF-1 with conventionnal engines because of the delays in the thermo nuclear engines... In other words, it's a big VF-1 that was made because they didn't had any other alternatives, thus the designation 0, a pre-release of the VF-1 that wasen't finished in time.