Google Search Console data is sensitive to the dimensions you select when setting up your data source, and the resulting data might differ depending on this. Google give some explanations to this behavior here.

The Performance View breakdowns in the Search Console GUI correspond to data sources set up with a single dimension at the time. For your data in Funnel to be in line with views in the Search Console GUI you will have to make sure that the dimensions configured on your Data Source corresponds to the view in the Search Console GUI.

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