Great points. We've actually talked to folks whose total fees were about 6% after all was said and done. It's crazy, but it does happen.
In your example, what I'd ask is if the web studio would be willing to pay $400 to get that $10k weeks earlier than they otherwise would have. That might be a good cash flow outcome for them.
All that being said, you're exactly right, the fee structure makes transactions of a certain size not make sense if you're doing more regular invoicing. That's why we want to add more payment methods over time that are lower cost.