It involves recurring audits of all systems in contact with cc information.
While I've never used stripe, i doubt they'd let you use that API without the certificate, as they wouldn't be able to do the aquiring for illegitimate transactions such as that. They could lose their status as an aquirer if they did that knowingly, and that would make it impossible to process any visa/Mastercard transactions.
You're more likely to encounter a simple scam/phishing site then a legitimate shop that let's cc information onto their servers. And that's honestly the only danger apple pay protects you from.