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...
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.
