When typeof object, the Object.is being different from === would be surprising a lead to bugs. This is especially true when objects can be added to weak collections.
Currently the tools doesn't have a specific warning for this situation. Example
Allowing Box(42) is different from allowing Box(#{}) in the case where typeof #{} === 'object'.
Also I think the message makes strong assumptions:
If primitives can be stored in a Box, then code checking if a Record/Tuple transitively contains an object can no longer be performed with a containsBoxes predicate. Instead the code will need to also check the contents of the boxes.
We could imagine a different predicate, aka Box.hasBoxWithIdentity or Object.containsObject (with identity bearing object being implied). Similarly I would precise that the alternative would be to recursively check the content of boxes.