If I understand you correctly, the in_layer and in_symbology_layer have different values and/or number of features. And you want the in_layer to have the symbology of the in_symbology_layer, but with the values from in_layer.If you uncheck 'All other values' in the symbology tab of the in_symbology_layer in the ArcMap user interface before running ApplySymbologyFromLayer, then you should get the result you expect. Or have you tried that already?Moreover, if you upgrade to 10.1, the AddAllValues function on the UniqueValueSymbology class should also do what you want.
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