Overlayering is (practically) not used anymore (extensions are used instead of layered changes of standard objects) and a layer is just a property of a model (and it's almost irrelevant).
Code and metadata is the same for all legal entities, because a legal entity is just data in database.
But you can change the runtime behavior based on legal entity. For example, you can use security to hide controls in some companies, or declare some fields or logic as applicable to a particular country only. And of course, you can write code to do things like hiding controls based on a parameter (which you can configure differently in different legal entities).
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