Just as Spider fac has natural weakness to Air (400 metal for mediocre AA!!!) so too is it ok for Gunship to have weakness to Amphib.
The heart of the principle is that factories can have glaring flaws against certain other factories as best-counter-unit specialities should be spread throughout the factories.
Best units per role by factory:
Jumpy: Best Fire unit, Best Land AA unit
Hover: Best Anti-Shield unit, Best Anti-Heavy unit
Spider: Best Skirmisher Unit, Best Scout Unit
Cloaky: Best Raider unit, Best Harass unit
Shields: Best Disarm Unit, Best Kamikaze Unit
HV: Best Assault unit, Best Paralysis unit
LV: Best Riot unit, Best Long Range unit
Shipyard: Best Sea AA, Best Torpedo unit
Amphib: Best Transport unit, Best Slow unit
Air: Best Economical unit, Best Air AA unit
Strider: Best Shield unit, Best Detriment unit
Gunship: Best Commsnipe unit, Best Trololo Unit, Best Deathball unit, Best Screamer Bait unit