There's some good points on here, and I always thought the stock remap is to try and cover as many bases as possible, based on what that projects goals are, there will be a compromise in performance to try and achieve better MPG etc if that's what they want for that model.
However, I haven't heard anyone mention their marketing strategies or costs, remember that in many cars or particular model cars from any marque, it is only one in a wide range of cars marketed at a different target audience, we've seen a lot of engines (especially in the VAG group) used on so many platforms in various states of 'tune' with little or nothing done to the engine. If the same engine, or other engines in the range produced very similar output and results to other engines then there wouldn't be any point in having that in the range.
The stakeholders and shareholders calling the shots won't simply say 'make this model perform the absolute best you can', I would imagine there's a list of acceptable parameters and goals, and that's what they try to get to, like any project. It's also as much about how much time they have to spend on R&D on a certain project as anything else.
Lets also not forget how many different legislation and local laws they have to comply with such a smog laws in so many different countries of their target market.
So, I don't think for one minute it is as clearly cut as a lot are suggesting.
Lets take aftermarket headers for example, they are known to make gains on the M113, yet you will still get people in the 'Mercedes and AMG the huge company they are know what they are doing' camp. Yes, they do know what they are doing, but that doesn't mean they are going to spend a massive chunk of their R&D budget or manufacturing budget in producing the best headers on the planet for that car.
As with everything that a company produces to make a profit, there are always compromises and other hidden agendas that we know nothing about.