this has been reported before on V6 - and storing all the audio data inside the CPR isn’t satisfactory for larger projects…your CPR size soon becomes unmanageable. Saves can take several minutes. You say that the ARA standard ‘recommends’ but that is not the same as ‘demands’ ?
Re: portability - I think this is a non issue, as long as it is inside the project folder in a clearly labelled folder then I can’t see why it is any different from ‘normal’ audio - there are even other areas of Cubase/Nuendo that don’t follow this standard…
Previously you have suggested people use Git or Subversion to manage this…I really don’t think that is a sensible solution 