There doesn't have to be entitlements or anything - it is not a technical problem and doesn't require a technical solution. Apple can just tell its app reviewers to skip the "alternate payment methods" issue when reviewing apps covered by this ruling.
Entitlements are a permission system, equivalent to Android's own. Your app lists what device access it needs and it only gets what it asks for and no more. Apple also uses them to audit or gate off device access to certain things - i.e. if your app requests the network extensions entitlement, then App Review is going to be asking why your app needs to be able to MITM all device traffic.
Apple appears to be using entitlements entirely to flag that an app is using third-party payments, which is kind of a hack as there is no way for iOS to prohibit you from offering them to begin with. But this is the standard way of asking Apple for extra permissions, so I can see why they're using it. The separate app thing is there specifically so that Apple can technically enforce that apps only get third-party payments in the Netherlands and nowhere else.
The alternative would be for app developers to check for themselves if they're in the Netherlands and only offer third-party payments if that check succeeds. But there's no (easy) way for Apple to verify that your app is compliant; app developers could totally Volkswagen them. Or at least this is the pretext Apple will use to justify making compliance as friction-filled as possible.
Entitlements are part of code-signing and allow access to restricted software or hardware features - they're checked at runtime before granting access.
They make zero sense when it comes to stupid policy like this though.
