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But why does this make them more money than offering separate upgrades at higher prices?

I do think there is a price discrimination story here, but there are some details to be filled in.

It's not obvious to me that Apple does make a significant amount of money by selling upgrades. Almost everyone buys the base model. The other models are probably little more than a logistical pain in the butt from Apple's perspective. Apple has to offer more powerful systems to be credible as a platform, but I wouldn't be surprised if the apparently exorbitant price of the upgrades reflects the overall costs associated with complicating the production and distribution lines.

It’s not about the price of upgrades though, it’s about their bundling together and the ridiculously stingy base specs that often make the upgrade non-optional. People who buy a base MacBook Air probably aren’t thinking about keeping it for 8 years or using it for heavy workloads.

Sure, but bundling them together reduces the supply chain complexity and reduces Apple's costs. If the options were more fine grained, Apple would sell even less of each model and it would be even less worth their while.

Also, I have seen lots of people on HN complain about the price itself, even if it's not what you yourself object to.

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