You can use the territory design tool + explode multi part feature to separate your data into pieces of 999. The use arc py. Although I am having trouble because the summarize by elevation tool doesn't automatically save the output to a gdb. It just gets added to the map.
arcpy.agolservices.SummarizeElevation(2, "zip5", "30m", "NO_SLOPE_ASPECT")
arcpy.agolservices.SummarizeElevation(3, "zip5", "30m", "NO_SLOPE_ASPECT")
arcpy.agolservices.SummarizeElevation(4, "zip5", "30m", "NO_SLOPE_ASPECT")