First off, if the DID run half express then the would obviously have to take over the local service. Yes, there would be merging delays.
Technically, the Bypass wouldn't necessarily be a waste if it went to Rockaways because there would be Direct Express service that goes straight into midtown.
As for a QB Local on the RBB, it could just terminate at either WTC or Houston St-2 Av
And it would ultimately be a wise Decisionto convert Woodhaven Boulevard into an express station of which the would merge onto the local tracks to RBB and an open door for a LIE subway line