Base Model MacBook Pro (2.2, 16GB, 555X, 256GB): $2399
560X Upgrade: $100
512GB SSD Upgrade: $200
Total: $2699
TOL Store-Bought MacBook Pro (2.6, 16GB, 560X, 512GB): $2799
560X Upgrade: Included
512GB SSD Upgrade: Included
Total: $2799
Price Difference: $100. So the 2.6GHz upgrade is $100 without the education discount.
One thing to keep in mind though, is that the relative price of the upgrades are different in different parts of the world. If the price difference were $200, would you still consider it a no-brainer?
In your calculation, the relative price for the 2.2->2.6 upgrade is 3.7% on top of the total cost (100/2699). In France and Germany it's 4.4% for the same comparison. In Finland it's 4.2%, in Denmark it's 3.8%, in Sweden it's 5.4% and in the UK it's 3.1%.
The actual value of the performance gain, I would say is something like $50. So in my view, you're always overpaying for what you get. But when you're paying $100, you're only paying 2X the value, and it's only $50 more. Big deal. But when you're paying $200 for the same upgrade, you're paying 4X of what it's worth. Do you agree that this makes a difference, and that the decision to upgrade or not may vary depending on your location?
For the 555X->560X it's similar, only in my opinion it's far worse. I would personally value the performance gain from the upgrade at ~$20. In the US you're paying $100 for this upgrade. So you're paying 5X of what it's worth. I mean... I can imagine use cases where every point performance gain counts. It's just that none of them apply to laptops, and even if they did you'd certainly get an eGPU instead. It's not the end of the world to get it, it's just a really really poor deal.
The SSD and RAM upgrades are similarly overpriced, but here it's at least easier for the upgrade to translate into some perceivable value. More RAM may mean you can solve larger problems. Sure, you're overpaying for the privilege, but you're still gaining a fair bit. More SSD, while you can always get by with external drives, having it inside the laptop is kinda the point of the laptop, so there's at least some decent value there even though you're still overpaying.
There's often the argument that if it's a business expense then it doesn't matter. Sure, the value of money becomes a lot smaller in that scenario, and it's effectively like having infinite money for the purposes of buying an MBP. So with infinite money, just pile on the upgrades and don't worry. But I also don't think people with infinite money are the ones debating in forums on whether to get a $100 upgrade or not.