Pricing works best when aligning with value instead of costs. In general you should also try to align your pricing with value for better margins (especially if you are have a monopoly condition).

The rationale is that Stripe believe that a small percentage will align better with customer acceptance of pricing than a flat fee per invoice, which allows them to capture more dollars from the relationship.

I firmly believe that transaction fees (incl invoices, etc) should be fundamentally a constant flat fee. Whoever builds a competitor to Stripe will blow everyone away.

The cost of transaction is the same. Customers are being robbed in day light with % based transaction fees since the dawn of time.

This entire industry is begging for disruption.

Transaction costs are not the same price per transaction. The major costs for most transactions are the risks (credit, irr, fx etc) associated with it not the fixed costs of infrastructure.

Those costs go up with the value of the transaction.

Good points, this was my oversight/ignorance. Surely it is not 100% value-based costs?

No. And you can do pricing that’s flat if you are really good at risk management but note that means the price for smaller transactions begins to subsidize the big ones.

See Atlantic Monthly vs Wise for different pricing types in fx transactions as an example.

Until you want value-based fraud prevention layers like insurance. Keeping fixed fee would knock that out of alignment. But perhaps your point would be that should be some sort of opt-in higher SLA tier so the transaction layer fee is low but the insurance etc. add-on layers are variable.