I read somewhere that the SV-51 was designed for combat since the begining and was more stable during battle, able to hover and with VTOL in fighter mode. However, it consumed its fuel pretty fast due to its engines and had slow transformation times.
The VF-0 on the other hand was a rushed combat capable prototype, with little underwater operations capacity, no outerspace operations capacity, overheating engine problems, low ammunition and no VTOL in Gerwalk mode...
All in all, the VF-1 is waaay superior to them, despite the lack of passive stealth. I don't think is fair to put the VF-1 in the same league of the Macross Zero valkyries...