For one thing, they fit. Even a kaiju fits inside of the T2 vehicle factory. For another thing, they'd bring more interesting gameplay to both factories. Having hovertanks in T1 naval would mean that there's a way to raid naval that ignores torpedos, and having a kaiju buildable by T2 vehicle factories would allow for more of a step-ladder between T2 and Titans. Thirdly, there's no logical reason why whey wouldn't work this way.
Cool idea. Already wondered about that point when I tried the new naval units. If you want a kaiju on a lava world, then it's just kind of a hassle having to build it on another planet with water and a T2 naval factory. Won't even be viable more often than not. Combining hovertanks and Kaijus is generally interesting since they are both faster than bots. Would like to see that change. On a similar note (which was already mentioned), it would be nice to be able to build the ares with T2 water for similar reasons. Just adds to the strategy and gives you more strategical options. edit: Otoh, I assume bulding animations are going to be tricky, not sure if a Kaiju fits into a T2 vehicle (or bot?) factory. It's also important to note if the change would weaken the impact of T2 naval (or even air) tech, if you can go for a T2 vehicle factory and get the benefit of both high tier vehicles and a formidable T2 ship.
As a parallel to this idea, it'd be interesting for the T2 vehicle and naval fabbers to be merged into one T2 hover fabber.
I don't know about this. I just spent a game on Meso abusing the fact that torps couldn't attack hover tanks to wreck my opponents eco in a way he couldn't really counter. I'm not sure having to build two sets of PA's already overly weak defensive structures to protect any area is a good thing. We need hover to project strength between elements and prevent games from dragging on when someone turtles up in a lake and also to allow people in a smaller element to fight back, but lets not exacerbate the negatives of this. In the extreme case hover makes the commitment to land or naval unimportant ruining the purpose of terrain variety in the first place. It should be weaker then standard units.
Since it is a T2 Hover BOAT and T2 hover TANK I think they should stay in the relevant factories. If we had only one option I would agree.
It should be different than standard units; fill a different role. I'm not a fan of hover units only being useful when their ability to hover can come into play however, just as I'm not a fan of amphibious units being useless unless they're being used for amphibious assaults. It's a thing called multiple roles.