1. Why aren't the heritage ability score bonuses balanced between each other?
They kind of are in a slightly complicated larger-picture sort of way. With the content being pretty ranged focus a Dex bonus would have been a prime pick. But Str/Cha are secondary scores that provide a little help with melee/maneuvers while Int/Wis are dump stats. So they were adjusted to +3 to make them more appealing and then Chaos refused to conform (because skill points are even less useful than will saves). I didn't really want the Feat to carry the weight of poor ability bonuses.
2. A bonus feat is almost always going to be better than a couple of cantrips, even with the discipline restriction.
Is it? Well, I suppose it's kind of a specific example but if you were a Warblade would you trade a bonus Feat to access Devoted Spirit?
3. Does this require referencing the D20 Future book?
Nope. It's technically modified Modern content, everything you need to know is in the chain of posts. Mech & Tech got a grammar update thanks to someone else but if you'll recall even Magitech said "This works similar to mecha as presented in d20 Modern's Future supplement with a few minor changes." & "[And unlike d20's normal mecha, it has an infinite number of equipment slots but cannot be equipped or modified by anything other mean than what is granted through this class." because I feel the connections are helpful if you happen to know them, not because it's necessary.
4. Song - Blue - What counts as a regional shift?
Ooop, meant Planar.