Re: a little over-engineered....
That system actaully has 3 resonators - two before the airbox (and a weird, little dead-end 'pipe') and one after the airbox.
Bolt placement is purely for ease of assembly. These cars are not designed to be taken apart afterwards.
The intake is much smaller in diameter than any of the CAIs out there, and yes, it does need a little more revving to get the best out of a CAI - but once you do rev, it's magic between 3,000 and redline.
The stock system is torque-y lower down because most people are shit drivers, can't balance revs and clutch, and nearly stall it every time they take off or roll round a corner 1 or 2 gears too high. That's what Mazda design the intake to get around. And the space, as mentioned above.
They could easily put a CAI in stock (especially with the electronic throttle body on the 06-07 C-Series models, as the CAI is now silent) but they don't.
They'd also run a greater risk of morons hydrolocking while driving through floods...