. . . automotive manufacturers must engineer a design with a "safety factor". . . .
those safety factors can be substantial; and most basic performance modifications are a game of reducing the safety factor, without going too far
It's the law of physics.....an engines air intake is directly related to how much air it can physically suck into each cylinder....nothing more, nothing less. The only thing that changes the rules is if you significantly increase the RPM or install a blower/supercharger...Ö because you are now force feeding the air above atmospheric pressure
The basic physics is that all fluid flow is driven by pressure differentials; there is no such thing as vacuum, only less pressure; the air fuel mix is actually pushed in by the atmospheric pressure that reaches the intake valves; and the point of any intake improvement is to reduce the pressure drop through the intake so that more air/fuel mix gets pushed in through the valves. Any measure of flow (CFM) through a system such as an intake is meaningless without the corresponding pressure drop; because the point is to reduce the pressure drop; with zero being the best theoretically possible (but never achieved). That said, for practical purposes, the pressure drop through the stock intake is pretty low, so there isn't much gain to be had; but there is some.
One sees posts here on the forum regarding bolt on hardware and issues with canned tunes. This is one example of problems and potential engine damage. Lots of posts on quality made mustangs breaking, for no reason? Sure!
With minor "bolt on" mods or tunes, the reason is not the increased output of the engine, but instead "bad tunes" that do things like advance the timing too much, or lean the mixture too much, which causes detonation or overheating, which breaks things. Or bad parts that simply do not work right; or a tune that is not correctly written for the parts used.