xlink:href is different to other ClientProperty mappings because it is used to express an identity relationship. For a one-to-many relationship, it is expected that multivalued xlink:href ClientProperty mappings result in multiple properties (leaf nodes), each with an xlink:href attribute.
The app-schema plugin fails to encode multivalued xlink:href ClientProperty as expected, except in the case of feature chaining. The problem is that new leaf nodes are not constructed after the first of the multiple values, resulting in a single leaf node having the last value (each subsequent value overwrites the attribute on the leaf node). The workaround, using feature chaining, cannot be implemented for properties with an empty content model (i.e. reference-only types).