The rclone webGUI just uses rclone normally (basically just runs commands for you), so it will use any flags that you set for whatever process you launched rclone rcd or --rc with. Thus, if you want to use --drive-server-side-across-configs=true , then just add this flag to wherever you launch the webGUI.
Alternatively you can just set
server_side_across_configs = true
directly in the rclone.conf file for each of the Gdrive remotes.
(note that this only works for backend flags - not general ones).
Sorry, I haven't found a way to do this either. the webGUI is still fairly early in development though, so expect that some stuff like this may be missing.