Can an airport cross subsidise an airline, even if they own it?
They can cross subsidise for as long as their share-holders (or creditors?) can stand it.
With Ryanair/Charleroi the problem was that the airport is owned by the state, and it is unfair state subsidies to business that the EU gets worried about.
Unless a private company is engaged in predatory pricing with the intention of putting another company out of business, then the competition authorities aren’t too fussed about what the private sector gets up to.
Not only do the owners of Manston have no obligation to be even handed in offering subsidies to other operators (charter, full service, lo-co or whatever) – if they thought it would threaten the viability of EUJET, they are quite within their rights to say no to anyone else who wants to fly there.