FWIW, my answer that’s marked as the solution (even though it’s a workaround) has been fine deploying across multiple environments, including management with ManageWP, since ACF Pro 5 came out. There have been no issues.
Hey peeps, here’s a quick fix to add a licence key on theme activation: https://gist.github.com/mattradford/6d5b8f3cd11ce1f62480
It would be nice to have an official solution though.