My understanding is that your claim is no true. Sure, some horse power upgrades are hardware within the model, but some are just bit flips in software.
No, that would require building the car to spec. The savings here is that the car is already built, and you see the blue car with the extra so-and-so, and they then chip it to what you paid for.
Having a blue car with extra so-and-so in every horse power engine would mean they'd have to stock that much more.
If the same engine can run at higher RPM it could mean that it needs better tolerances to achieve it so they bin the better parts for those engines.
Other things might also be slightly different like slightly different fuel injectors, seals etc. that can handle the more demanding workload.
You can tune virtually identical parts to perform differently but that process usually has a cost to it.