No business can sell anything with zero markup and not lose their shirt. Apple needs to pay for shipping, labor to assemble, engineering, test and validation, support and warranty (OEMs usually sell without warranty). Then the retailer needs to take their cut on that for rent, "free" shipping, credit card fees and fraud, theft, returns, labor, power bill.
Let's break this down.
1. OEM boxes are single pack processors with no warranty. OEM tray orders come in 1000 packs. The OEM price of a single processor in a cardboard box can be as much as $40 less (sometimes more) than retail packaging. At scale, OEMs get major kickbacks. Intel is known for offering major kickbacks to OEMs to secure their business. The $899 processor in the base Mac Pro may cost Apple a mere $200 each instead. $899 is the retail pricing for general consumers. An OEM single pack may cost you $750-800.
Retail 9900K costs around $488 right now. OEM may set you back $470 for one processor, no warranty. An OEM tray of 1,000 9900Ks may cost around $450 each, however, a major OEM like Dell, HP, Apple, MSI, et al. can negotiate this way down to $100 per processor, for example. No major OEM is paying the list price. Ever.
2. Labor to assemble. It's either a socketed CPU or soldered to the logic board. This isn't very difficult to do. Most of it is likely mechanized.
3. Engineering is a sunk cost. It doesn't go up or down. It's there to stay. Sheer number of moved units splits the costs up. Test and validation don't take hours like you think they do. And if the test and validation is as thorough as you believe they are, Apple wouldn't have so many issues with their hardware that popup so often.
4. Apple is an OEM. They have a warranty on their products that can be extended via Apple Care. Other major PC OEMs also have similar warranty layouts. Do you mean Intel and their OEM processors? You're right, except Intel places the warranty on the retailer or OEM you purchase through. In other words, if your Intel processor fails, it's on Apple to fix it, not Intel. And that's if your warranty period is still active.
5. Retailer rent? When did Apple begin franchising stores? Apple corporate takes care of that. How much do you think Apple spends on shipping? UPS and FedEx likely charge Apple a nominal shipping rate and they have one of the best logistics in the world. In the same way I can order something off of Amazon right now and have it by my door at 5 AM tomorrow morning. Amazon can only do this in a few areas. FedEx or UPS can do it nearly anywhere. You're blowing this up to be a high cost item when it isn't.
6. You bring up credit card fees, but which ones? Some are negotiable with the major systems, MasterCard and VISA, other fees are tacked on by institutions; BoA may charge you more for running a customer's card than JP Morgan Chase; Wells Fargo may charge more than both combined, etc. Some fees are required and non-negotiable, but these aren't pricey but they do add up. Then again, merchant accounts with either major credit system come in various setups. Apple could simply pay a bulk fee per month because they move so much and have so many transactions. Apple could pay $0.50/transaction and pay a flat fee of $50,000 a month.
Apple sold just over 1.5M computers per month in 2018 alone for a total of 18.2~ million computers for the entire year. I'm fairly confident Apple makes hand over fist and whatever fees you're proposing are negligible costs for the likes of Apple. This isn't someone's front yard lemonade stand. Do you think one of the world's wealthiest companies can't stomp around and propose what they think they should pay?
Amazon has, on a whole, gross margins of 40% and net profit of 5%. That means they need to mark up 35% just to break even.
Amazon is an e-tailer. They don't focus on a segmented line of products. Amazon sells other people's products. They also have their own line of products, but they're niche and if they're not their niche products, it's Amazon Basics, which no one really buys.
Amazon sells e-books. None of which they write. The only portion of their books segment they make significant profit on is likely their own imprints, of which they own about 10 IIRC. Kindles are sold at cost. Amazon web services are a whole other story, and it's fair to say it's a niche line since a fraction of the population is using them directly. Whereas they may use services that utilize Amazon's web services.
Amazon and Apple are not very similar companies. I fail to see why you're comparing the two. Had you compared Amazon to Costco, I'd have seen what you're trying to do, but alas I do not. Compare Apple to Dell, HP, Asus, Acer, Samsung Technologies, etc.
These are tech focused companies that create mass produced and mass used products and are known for their product lines. Dell is known for their laptops, their desktops, their servers, their professional IPS monitors, etc. The list goes on.
Amazon is a place known where you can buy batteries, order some pancake mix, organic treats for your dog or cat, toys for your kids and some Tide Pods to give to the neighbor's dumb children all in one order.
Edit: Were you comparing the two because they have similar profit and 12 month trailing numbers? I mean, that's fair, but their costs expenditure isn't the same at all once you look at their actual costs. Apple spent something like $15B on R&D last year. Amazon spent maybe $30B last year on R&D. Amazon spends a lot of money making sure customers are happy, including giving out gift cards because items came damaged or later. In the case of damage, they may tell a customer to hold onto it and send out a new one to make the customer happy. Regardless of whether or not they're a Prime customer. Apple isn't sending out new hardware because your box was beat up but your product is relatively fine. Arguably, Amazon likely incurs far more fraud than Apple does, and thus writes it off.
Amazon operates a lot of services, some of which cost a lot of money to run. Even if you compare them at a pure tech level, Amazon and Apple are leagues apart. One is a world class provider of cloud services, the other is a world class leader in hardware that excels beyond what the competition can come up with at the best of times.
To give you an idea of costs expenditure on cloud alone:
Apple has roughly 5 or 6 data centers, with one in the works right now and one following it. Globally, Amazon has close to 80 or did in 2015 according to a leaked document. Apple also colocates. Amazon doesn't.
It lists 38 buildings in Northern Virginia; eight in Seattle; eight in the San Francisco Bay Area; seven in northeastern Oregon; seven in Dublin, Ireland; three in Luxembourg; four in Germany; nine in China; 12 in Japan; six in Singapore; eight in Australia; and six in Brazil.
Go run a business yourself and see how many little things add up.
I do. We've taken multiple steps to lower our outgoing costs, especially power usage. In the last few years we've lowered our yearly electrical costs over two locations by about $60K a year. Credit card fees are not something we worry about (we don't process them nor do we ship a tangible product). We pay other large fees.
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