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It is not possible to have ModeShape return a different value from Node.getIdentifier(). ModeShape always returns the node's UUID, regardless of whether the node is 'mix:referenceable'.
Of course, you can always define any property and treat it as a unique identifier, and use a query to find the node (or nodes if not unique) with that property value. For example, you could define a node type similar to 'mix:referenceable' with your custom identifier property, and add that mixin to individual nodes and/or as a supertype for your other custom node types. Unfortunately, the JCR specification doesn't really provide a way to specify that each value defined by a property definition is globally unique, so if uniqueness is important, you'll just have to use some type of value that is unique enough for your system.
I hope that answers your question.