"So stripe here would charge an EU card from its EU entity, US from the US, GB from GB etc etc, regardless of where the merchant is actually located. Maybe there is something fundamentally different with the workings of Visa / MC payments and clearing though that means this is not possible?"

Not really. The transaction happens on the country the merchant Operates.

If you are a merchant within the EU and stripe accepts a txn on your behalf, if that txn is from a card issued by a UK institution you will be charged the extra fee.