I'm not familiar with the complete legal structure of Manx2, but they do operate all their flights under the NM designator, which means that they must have a basic AOC. Otherwise they would have to sell the tickets under the code of their operating partners.
That's apparently what they do. If I am not mistaken, "NM" is the designator of FLM Aviation, the German airline that over the years has operated most of the flights for Manx2 with their Dornier 228s and Metroliners. Not sure how the legal construction is in relation to VanAir (the Let 410 operator) and Topfly (the Metro operator) as they operate under the "NM" designator (at least in the marketing stuff published by airorts nad Manx2) - maybe technically FLM sub-leases their aircraft when operating Manx2 flights.
As for the T&C of MAnx2, I find them rather bizarre as the passenger as a partner to the contract apparently is in no position to ever find out who he has entered into a contract with. Because at no point he is told who will actually operate the flight although, according to the T&C, the operator is the partner to the contract. At least in my jurisdiction, this uncertainty would void the contract.