"What could they do that a Typhoon squadron, supported by tankers if necessary, at Luqa could not do? There is no need to operate outside of allied airbases and in international waters in this situation"
Except that Luqa is not an allied base and Malta is neutral and non-allinged although a EU member.
Just a thought but as it's airspace has already been violated once by two Libyan Mirages (whose pilots were seeking asylum) what if the bulk of the Air Force has remained loyal and the next that might arrive have other ideas? Is Malta looking for air cover?