When I ⌥ Alt LMB on a transformations property, I can change multiple the property for multiple object with once input action. The property turns blue for the duration of the operation.
Is there a way to make this work for custom properties?
I don't believe it's possible by selecting both of the object. For a simple reason, one of the object may not have the property.
If you want to change multiple property at once you can add a driver between the property of the two (or many) objects.