When you set a factory to wait it actually stops building the unit. Assisting cons/nanos will finish the unit though (that was the old behavior also in 85). But now a factory on wait will spawn another nanoframe when cons/nanos finished the current unit (unlike 85 where a factory on wait did not spawn the next nanoframe). That nanoframe is of course build by the assisting cons/nanos. So actually you are still keeping producing in a wait'ed factory even though the factory is not building itself.
Tested in BA765.