The purpose of the extension API is to create regular, context-free output (extended form) for algorithmic processing - this is exactly what you want to do. So yes, you have the right approach; you should not miss any extremes, as I understand you. Once you have JSON-LD in extended form, you can easily follow @ids (and if you also need to do some kind of dictionary / ontology analysis, you can follow the properties, which then will be fully extended URLs )
dlongley
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