I guess this depends on what you want to achieve. Even with Sandboxed Play Services installed, you still have a more private experience on GOS than any other Android or iOS system (storage scopes, contact scopes, sensor toggle, upcoming app communication scopes, etc.). So full convenience would be if you put everything in one profile.
If you require to get notified when somebody sends you a message but you otherwise don't interact much with WhatsApp, I'd try making the WhatsApp user profile, allow it to run in the background and activate notification forwarding. You can isolate WhatsApp from everything else this way and use a different set of contacts without having deal with the struggles between WhatsApp and Contact Scopes. You'll get notified for incoming messages and switching profiles is just a minor inconvenience, especially if you use fingerprint unlock.
Can't say anything about the benefits of shelter since I never used or researched it enough...