Not a single programmer, manager, or any other central office employee gets paid out of COGS. There are
at least 50,000 of those. Same goes for real estate costs, legal costs, etc. Servers and their operations costs might go into COGS on the AWS side, but definitely not on the retail side.
Breaking out investment vs administrative cost is actually very hard to do. Is a programmer working on a new feature an R&D cost, or an administrative cost? What if it's a new service? What if it's a new product? What if it's a bug fix? What if it's a critical vulnerability? What if your programmer does all of the above at different times of the year? It's pretty much impossible to separate administrative overhead from research and development in tech companies, which is why they tend to not do it unless they are forced to. It's up to their shareholders or the SEC to force them to do it if it happens, which hasn't been the case for Amazon yet.
It is assumed that they would be turning a profit if they decided to just keep the lights on and not invest in the future. That's what they tell us, and that's what we see (new product and service announcements tell us as much). What we don't know from public information is whether they would be 10% more profitable or 10,000% more profitable. And that's before we know if their investments will pay off or if they become another perpetually subsidized program like Amazon Fresh. That's why Amazon stock is considered to be a speculative investment, whereas Google and Microsoft are more in the blue chip camp. My experience and hunch tells me that Amazon stock prices are at least 50% undeserved hype.