The issue isn't collaborating with your users and involving them in the design process - do that! It's awesome and it'll generally help you make better products.
The problem comes when you want to harvest intelligence from your users WITHOUT cooperation. If you need to do that to be "productive" ala Google, then yes, you are going to be hampered by privacy. That's a tradeoff for users to make, and it's only a real tradeoff when we aren't dependent on the moods of Google or Facebook but instead can rely on the underlying technological basis.
And you can be very interoperable and maintain privacy - but your users will need to choose to enable that interopability. Facebook can "promote interopability" by linking my Instagram and Facebook, or forcing me to use Facebook on Oculus and that is interopability - but it's sort of by force and not in a way that is acting with my consent. On the other hand, my email I send with Protonmail is perfectly interoperable - I can email anyone and get email from anyone, import and export emails and use whatever client I want - as long as I choose to allow it to be by decrypting my emails.