You have a solid point that demonstrates a unique perspective that a non-capped sport like baseball provides (and in my opinion, shouldn't be impacting the personnel balance).
I think there are multiple ways to look at this, but the competitive balance that a salary cap creates is merely a competitive issue within the league. If the owners of any club decide to scale back/up expenses for salary then they are making a business decision (Nintendo, to use your example). Speaking from a purely "sports" perspective, business decisions by the owner are more heavily impacted in a non-capped sport like the MLB versus the NFL or NBA.
If Jerry Jones (NFL) wanted to double his expenses on the Cowboys, it can have zero impact or advantage over another team. The same goes for NBA owners. Their business decisions (financially) can't exceed the maximum impact of all other teams.
Baseball is the only professional sport among the "Big 3" where money CAN get you a better team than someone else. Teams in the NFL/NBA could choose to under-spend the cap, but that would be ludicrous and they don't. However, NFL and NBA organizations can not gain an advantage by choosing to spend more money than other organizations. In the NFL/NBA it is more important that you have the best staff to select the right players and to develop them -- much more so than in the MLB.
Essentially, the fact that the business decisions of an owner even CAN impact the quality of a roster shows that a non-capped sport is more an exercise in business practices than it is a demonstration of skilled sports organization development.