Legacy:
The Maintain Spatial Index environment is not honored in ArcGIS AllSource. To have the same behavior as the Maintain Spatial Index environment in ArcGIS AllSource when running tools and workflows that perform insert, update, and delete operations on existing data in enterprise geodatabases, control of the spatial index can be accomplished using the Remove Spatial Index tool to remove the spatial index prior to processing and the Add Spatial Index tool to re-create the spatial index after processing.
The Append tool also supports this workflow with file geodatabase data.