setReplaceMethod() is just syntactic sugar for setting an S4 method on a
replacement function (read the function definition to see so). You can
set S3 replacement methods, and the S4 mechanism just piggy-backs on that.
So I understand that setReplaceMethod will not help.
I think the conceptual problem is that the assignment operator does not
actually do any copying: it creates a binding of a symbol to a value.
Any copying which occurs happens when the value is (potentially) changed.
I would be even happier if the cloning would only occur on any attempt to change the external pointer / proxy-object.
There is no provision for that to depend on the class (rather than the
type) of the object.
Mh, unless the internal copying mechanism would call a clone generic for non-atomic objects