The actual reason for the exemption is that they cannot impose the tax on non-EU operators, giving the non-EU operators a competitive advantage.
Presumably they already signed aviation treaties that do not allow for this.
> members of the International Civil Aviation Organisation (ICAO), including the United Kingdom, are prevented from taxing international aviation fuel, or any proxies for fuel, under the Chicago Convention.
https://researchbriefings.files.parliament.uk/documents/SN00...
https://www.gov.uk/guidance/rates-and-allowances-for-air-pas...