Of course there are always compromises made by the manufacturer, in the case of handling the choice is largely wether they preference ride comfort or outright handling, exhausts have legal considerations (as indeed do intakes to a lesser extent) - the manufacturer will obviously try to choose the compromise they think the majority of their customers would prefer (within their legal allowances).
My comment isn't so much to say that the factory intake has no room for improvement whatsoever, but rather than making essentially random changes willy-nilly without any real research, isn't likely to land you many benefits. Generally there is very little to be gained from messing around with the intake on an EFI car running the factory tune, and you may even take steps backwards if you just start hacking it to bits.
Manufacturers will often position their intakes to take advantage of zones of positive pressure at the front of the car, so in effect you get a mild amount of "boost" while the car is moving. They have wind tunnels and CAD modelling to find where these areas are - backyarders don't. Also, it's worth considering that the intake is only going to be as fast as it's slowest component, so unless the section of intake you're hacking is the most restrictive, you're not going to do much good - this is exactly why K&N filters are a scam, the factory filter is not a restriction to the system as a whole to begin with.
You may be able to improve on the factory intake, but to do it properly you need to actually figure out where the restrictions lie (by measuring them), and even then you'll probably need a tune to get any meaningful improvement from this extra air-guzzling capacity.
