For several of my plugins and themes I have code that basically does the same thing that ACF is currently doing. I do have one theme where field groups that are synced from the parent theme are then saved in the child theme so that they can be modified on a per site basis. This theme is currently not active on any sites but is is a model that I have been know to use.
I don’t have an answer for this at the moment
You might want to send the question to support and see if they can help you with a solution or perhaps add something to ACF in an update that will allow what you are looking for. https://www.advancedcustomfields.com/contact/
