Next step: ownCloud makes the desktop client incompatible with NC, modifies next 8.2, 9.0, 9.1 updates that they cannot be upgraded to NC any more? That would be bad for the whole community and people will rather turn away from this platform.
You should find an agreement with NC to share the development of some “core” apps and the clients unless you can’t provide a full support all by yourself (which currently no solution provides). I know both are very healthy and better and stronger than ever before.