Answering my own question, having looked at what I dismissed as an irrelevant post more thoroughly I spotted a potential source of the above. It appears the python3 recipes pyconfig.h is getting clobbered by the tensorflow recipe which I had previously built:
https://github.com/ribalda/meta-tensorflow/blob/7c0dba3f2fb95f4ece1535b3f3d7e5cc98361f19/recipes-framework/tensorflow/tensorflow_1.13.0.bb#L57
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