I dont know the ferry schedule but a morning one in from Split and a late one out to Dubrovnik. I was only okay with Korcula. The side trip only adds 1 hour additional travel time.
Cesky Krumlov with an early shuttle out of Prague then a late one on to Vienna also sort of works and adds 1.5 hours vs a straight train between Prague and Vienna. The advantage with the Cesky Krumlov detour is its door to door not port to port or station to station. From the shuttle you can see countryside. From the boat, water; but you can move around more.
I think its about time of year and personal interests. I loved Cesky for the river raft, castle theater, ambiance, architecture ... its so freeking pretty in the evening. Korcula was more of Croatia. Warm and comfortable. Both are expensive.