Why is it easy to circumvent your checkout flow? I would own the money transfer. If a developer doesn't want to build their own store, they probably don't want to bother implementing Stripe themselves either (and I probably have no clue how to estimate how many API calls I need).
Do your target customers really need payment gateway flexibility? The biggest drivers (I can think of) would be acceptance (by country & payment type) and transaction fee.
You don't have to call it 5%+, you could frame it as 1% + whatever the payment gateway you choose charges. That doesn't feel too egregious.