For 1) and 2), what option do you choose at startup? According to what you seem to wish, you should choose one of the hilited options:
If you don’t see this dialog when running WaveLab, press and maintain Control (Command on the Mac) pressed while launching.
For Master Section plugins, there is an additional option:
For 3) I am not sure what option you are referring to. The only one I have in mind, “Play through Master Section” is the option for Basic Audio CDs. AFAIK, this works correctly (when you start playback from the Basic Audio CD window).