Right - but those pushing for external app stores assume it will work that way. Instead... Apple's probably going to make some forms and demand manual reporting and commission payments.
However, it would be so contrary to the spirit, if not the letter, of the law that I expect any such attempts would quickly gain antitrust scrutiny and new legislation declaring that APIs and software included in a device may only be monetized at point-of-sale (with the exception of subscription plans marketed toward consumers). It is possible that a court would even see it as such a violation of the law's intended effect that they would step in.