> a) Will Apple not allow apps on the official App Store if they appear on third party ones.

The EU almost certainly wouldn't allow it.

> b) How will Apple collect their commission. There is nothing in the regulation that says that they can't continue to do this.

See Denmark which has an App Store carveout for in-app purchases within dating apps. Basically, Apple wants records and reserves the right to audit.

Considering this is more than in-app purchases, I would expect a requirement for an Apple Developer account and a legal agreement to get a process similar to notarization on macOS.