Manufacturers have big budgets and lots of resources. It is in their best interest to optimize the engine management systems to perform as well as possible in all areas of performance. That includes driveability, fuel economy, power, ignition timing, altitude compensation, hot starting, cold starting, warm-up, etc. While they must obviously make some compromises here and there, they do achieve a pretty seamless overall package.
With a totally stock system you would have to give up something (mileage, driveability, low end performance, etc.) to get something else like more power at the top end. And most chip "tuner" companies don't have a lot of resources and have to "reverse engineer" the stock chip and make an educated guess at what might be "better". Usually they don't do so well. If you get 2 or 3 % more top end power at the expense of 5 or more MPG and a "flat spot" just off idle and a lean surge at 30-40 MPH is it worth it? Usually not.
Most factory systems have enough built in "adjust-ability" to compensate for minor mods like uprated air filters and freer flowing exhaust.
If you do major performance mods that end up requiring more than the stock system can provide then a custom tuned chip and fuel system mods are in order. The ONLY way to successfully set up the system is with a dyno and calibrated fuel mixture measuring devices to program that chip for that specific engine. There is NO practical way to program a chip for an engine by estimation and therefore NO way an "off the shelf" aftermarket chip can be an exact match for any tuned engine unless that engines needs happens to exactly match the parameters programmed onto the chip.
I wouldn't put a dollar on the odds of that happening.
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