The idea that the ongoing cost of moving money between parties varies on the amount of money moving is very "sus" as they say. Whether they move $10,000 in a transaction or $3, roughly the same number of bits move, the same number of algorithms kick off, and so on. Is there a cost-based rationale for doing a percentage-based pricing model, or is it really "because they can"? I could brainstorm and say "fraud" or "def…
The majority of the current payment cost (2%+) happens when paying by card. But as you say a payment right now is just moving bits. The main reason why cards charge so much is due to Risk. If you read about "interchange fees" you will see how Visa, Mastercard, AmEx, etc. classify different cards into different levels and charge a different exchange rate for each of them.
But the thing is, this system and networks were created last century (around 1960) and nowadays there is better technology to assess risk and to perform the transactions.