There is no way that the average purchase costs $2.50+ to deliver, even amortized over the lifetime of the book.

Amazon can charge whatever they want; I just think they should be transparent about what people's net pay will be. It's disingenuous to advertise that you take a 30% cut plus "delivery costs," and then mark up the "delivery costs" to over 25% of the average book price. Apple uses a similar paradigm (processing fees do not come from their 30%), but they only deduct the actual processing fees.

Maybe kindles are manufactured at a loss and these delivery fees are then part of the device cost?

But that's not a "delivery fee", which makes it kind of dishonest. Amazon already take a fixed 30% cut, which ought to include any subsidy on the devices.

What does Apple typically charge in processing fees on top of their 30%? I’ve tried to find some information on this, and every source I’ve found says they only charge the 30%.

It's 30% plus the payment processing fees. It varies because Apple is clever about charging multiple purchases at once (which works to your benefit), but it's closely in line with processing PayPal, SimplePay, etc.