So in short it isn't a misunderstanding and they want to charge you per item for something that, for all intents and purposes, is like a single drop of water in an ocean.
Be aware that IPv4 is also still /extremely cheap/ - way less than $1/ip/year if you have any volume at all.
When people charge you for IP addresses, the money is for the effort required to deal with justifying them to your rir, setting them up, routing, and maybe to cover abuse (my experience has been that the amount of abuse work i have to put in to a customer correlates somewhat to the number of IP addresses they have) And yeah, probably a good chunk of profit.
The price of an IP, right now, has almost nothing to do with it's scarcity.
They want to charge you for the drop, the space in their RIB to store the drop, the maintenance effort required to keep the RIB entry configured correctly, and the ongoing support costs of people who do things with their Linode boxes that require more than one IPv6 address.
A drop of water compared to the volume of Earth's oceans is about one part in 2^84, so your analogy is a bit of an exaggeration, as there are only 2^64 /64s to be handed out. Still, there are plenty of allotment sizes larger than /128 that are still not scarce enough to bother charging for unless you have some other leverage (lock-in or a unique advantage on some related product).
They want to charge you for the static route you've added to their (finite) router memory, and the administrative overhead for adding it when they don't have the process automated yet.
When people charge you for IP addresses, the money is for the effort required to deal with justifying them to your rir, setting them up, routing, and maybe to cover abuse (my experience has been that the amount of abuse work i have to put in to a customer correlates somewhat to the number of IP addresses they have) And yeah, probably a good chunk of profit.
The price of an IP, right now, has almost nothing to do with it's scarcity.