Yep, Stripe prices its products pretty competitively and talks to many beta testers before we settle on pricing. I think even adding all this up, it's less expensive than merchant of record providers like Paddle.

Why does it have to be a percentage of your revenue? It’s doing exactly the same thing for a $100 invoice and a $10000 invoice, why does the latter cost 100x more?

Value. A service Y makes it easier to collect that $10000 invoice. Inversely, by not using a service Y, you might not see those $10000 or it will be more difficult to do so.

A glass of water has more value to you when you're thirsty.

Why not ? If you have small transactions you end up not paying a lot, and the more you make money the more you pay Stripe. If you make so much money that you can have your own tax system, good for you ! Implement it and don't pay Stripe :)

Fixed price schemes would be less fair for small businesses that want to grow. Stripe helps you to grow, so that your company becomes the one big enough to "subsidize" the small ones after benefiting this pricing in the first stage