Currently it is already possible to select a python toolbox (*.PYT) in the project option dialog, but it is not possible to actually set it as the standard project toolbox.
Please support python toolboxes (*.PYT) to be set as the project standard toolbox.
This will be allowed in ArcGIS Pro 3.0, in addition to the default toolbox for new projects using our new ATBX format.
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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