Indeed you are correct and that's why it's generally simpler to use a service that acts as a reseller - i.e., they are the vendor of record. This means you shift all of the responsibility to them and you don't have to deal with it. Using the likes of PayPal / Stripe is not a good idea because you will be responsible for VAT compliance and with the newly introduced EU legislation, it can be a huge hassle - you need to deal with the MOSS at least. If you're selling software, I can recommend FastSpring - it's what the majority of Mac software houses use, it's highly customisable and they've been around for years.

Furthermore, if you're UK based and use a non-UK marketplace / reseller, then the revenue you receive from the reseller lies outside the scope of UK VAT and you don't have to do anything [1]

The reason why most EU developers on the App Stores don't deal with VAT is because the vendor of record is Apple Luxembourg, thus lies outside the scope. And that's precisely why Apple requires VAT invoices from Luxembourg-based developers.

[1] https://www.gov.uk/vat-how-to-work-out-your-place-of-supply-...