I believe ApplePay requires TouchID.
> To help ensure the security of Apple Pay, you must have a passcode set on your device and, optionally, Touch ID. [...] To send your payment information, you must authenticate using Touch ID or your passcode.
By feeding numbers into the scanner instead of fingers, you can accomplish the same effect as feeding random strings into a password box. Further, it's also possible to take fingerprints through social engineering, or by getting at the database of a company that uses fingerprints as security. Five bucks says someone's already storing a bunch of fingerprint data as plaintext.
Isn't this exactly why they DON'T allow you to use the iPhone with a potentially tampered with HW/TouchID -- e.g. the very feature/issue we're discussing?
The fact that you need to enter PIN right after boot, just shows that they use "two factor authentication" to make it even more secure.
It doesn't IN ANY WAY show that TouchID is "the less secure authentication" method of the two.