Currently GP tools are set to run on all records in a feature class, or in the case of any having been selected, the tool will only be performed on those selected features.
In the various dialog boxes, it should be possible for ESRI to have them point out when the GP tool is set to run on just a selected subset.
@KoryKramer Another fix was also applied to the 3.0 release. When a definition query is applied to a layer, the selection is cleared if the item is outside of the definition query.
So now, order of when the selection and definition query are applied will not affect the tool results.
This functionality has been added in ArcGIS Pro 3.0. See Ideas in ArcGIS Pro 3.0 to see this and all of the other ideas you can look forward to when you upgrade.
Also be sure to check out the What's New documentation: https://pro.arcgis.com/en/pro-app/latest/get-started/whats-new-in-arcgis-pro.htm
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