I'm pretty sure she misses all her shots. Any time she actually gets close to hitting him, he just transforms and flies away quickly (watch it again, everytime he seems to get grazed, it's actually the yellow burst from his engines). Meanwhile Alto takes his leg clean off with a short burst. It seems that overall manueverability (mainly due to amazing acceleration from the four engines) is the VF-27s main advantage, the reason Alto was able to get the leg was because he used his missiles to confuse Brera and surprise him. Also, despite the VF-27 being able to accelerate faster, the VF-25 seems to be able to catch up.
All things taken into consideration, while the VF-27 seems to pack more tech than the VF-25, it seems that SK means for them to be evenly matched (similar to the YF-19 and YF-21 from Macross Plus).