If you start with flexible starting locations, then Na'vi get a regular Human colony pod -- I don't think there's a way around that. The thing is, though, the way I've fungused up the worldbuilder you wouldn't want to use flexible anyway, because you'd have to go 10 spaces or more to find another non-fungus square you can build on.
The "special" weapons and armor aren't available later. For humans, the highest you get is 6 attack and 4 defense, for the Na'vi it's 4 attack and 2 defense. The 2 clan-specific special units (Toruk Makto for the Omaticaya and Thanator Rider for the Anurai) are 12/8 and 8/10, respectively, and I didn't want those weapons and armor being put on other units.
Hey, I just discovered something interesting -- the 18th and 19th rows in #UNITS (normally occupied by Battle Ogres Mk 2 and 3, respectively) automatically get fuson/quantum reactors, regardless of what you put in for chassis/weapon/armor. So, it is possible to have up to two predesigned units with higher-level power plants. Strangely, any unit placed in slot #20 (fungal tower, normally) will show as "already moved" when you first build it, and then the next turn its flag will turn red as if it's an alien life form.
In case anyone cares, I'm still working out problems and making changes. I decided to pre-design all available units and disable the workshop completely, and it's working pretty well as far as the AI's ability to function goes.