It would appear that SkyWork now offers connecting flights. For example, I noticed that Rijeka (in Croatia) could be reached from Cologne-Bonn via Berne for as little as EUR90 OW, incl tax.
My own experience on SkyWork (FCO-BRN) was outstanding. The flight was so memorable and the service so great (with a nice meal), that I awarded it 10 out 10 points! This is how flying used to be!