Posted a question in the board here that addresses this idea: https://community.esri.com/t5/arcgis-experience-builder-questions/can-you-control-output-layer-order-from-output-of/m-p/1637873#M20221
Right now, the layer order generated by a custom GP service is completely random when using the Analysis widget. When the tool is run in ArcPro (pre-publishing) the output layer order is set in the script and is consistent. This was a functionality of the WAB geoprocessing widget and should be added as an enhancement to the Analysis widget in ExB.
Please, please make this a thing!
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