Stripe may offer a polished and complete system but if SagePay or whatever are cheaper, larger enterprise clients will think twice, especially if they have the people on their staff capable of taking SagePay's APIs and making them look and work just as nicely as Stripe.

And it's an acceptable tradeoff to charge less per transactions if you're getting considerably more transactions than with a smaller client, and getting a big name partner to put on your landing page.

If I ran a company like Stripe of course I'd liaise with Microsoft or whoever and be like "yo, if I cut x% of transaction charges wanna use my service?" and boom I can say "Microsoft uses our service omfg!" on my website...

and then I have more big enterprise clients on the phone because they'll conclude that my product must work, must work at scale, and must offer something valuable to a big client like Microsoft.

That's probably why a lot of companies on their Pricing pages say something like "Enterprise? Get in touch" rather than simply giving a number. A client with huge demands might need prior preparation/augmentation to the architecture of your actual service delivery in order for you to keep up and supply your service to your existing customers, let alone pricing deals where an enterprise client may have bespoke demands or a special deal.