Unfortunately, there really isn’t a great solution available for this. When you have a flex field ACF creates a hidden copy of each layout. When you add a layout ACF copies that hidden version to create the new layout.
The correct solution would be to use the ACF JS API, see also: Adding custom javascript to fields. Because the repeater would need to be populated when the layout is added. Unfortunately I don’t now of any working examples of this to reference.
