It may rub some people the wrong way, but Matt speaks the truth. Gone are the days where the guys down at the factory were making stuff up and the quality of your engine depended upon the part-to-part variability of the springs that were on the line that day.
If you improve the "performance" of the engine one iota from the factory now, it's only because you define performance differently than they do. Within the box of emissions, noise, fuel economy, and engine part life, the factory setting will be absolutely maximum performance. Small manufacturers, and certain low volume products are an exception to this.
It's inconceivable that a guy poking around in the dark is going to find an improvement, even if he is an expert (or even THE expert). He can't know all the interactions or parameters he would need to know (physical or electronic) what's going on in there, and he simply doesn't have the time to test all the variations. High volume engines will have several lifetimes of systematic testing performed before they go to production, by the people that are holding the code book and the hardware blueprints.
It's certainly possible to increase (X) from the factory setting, but it will always come at the cost of everything else that the engine was tuned to meet. If you want to increase HP, torque, fuel economy, whatever, you can. But you will be giving up emissions, noise, fuel economy, HP, engine life, or other parameters that you are not optimizing for.
Matt's point was (I think) that it's not a given that you will even increase the thing you are after any more, at least not significantly. You may make a change that will presumably increase HP, only to run into an interaction that counteracts what you are going for. Further, the opportunity available to increase HP is much lower than in the past when factory designs were not as finely tuned.
It's more difficult to improve now, and there is less improvement available. People who really know what they are doing can get performance beyond the factory tune, if they have specific limited goals and are willing to give some things up.