If I'm not mistaken, most of the commands in blizzard's Addons scripts have calls to turn off/on ingame. You probably want to turn off just one or two of the effects, maybe? Well if you find what they are in the script, you can turn them off by calling it false in a call script event.
Right out of the script;
#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
# START Configuration 2
#
# You can enable/disable any add-on here if you wish. Set the value to false
# to disable it initially. To turn it on/off ingame, just use the Call script
# command with one of these syntaxes:
#
# $game_system.NAME_OF_THE_ADDON = true
# $game_system.NAME_OF_THE_ADDON = false
#
# where NAME_OF_THE_ADDON is the same variable as the one used below.
#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
So for example if you had
@BETTER_TILEMAP_UPDATE = true
Just have a call script event saying
@BETTER_TILEMAP_UPDATE = false
but this is for the SECOND configuration, a few cannot be turned off/on ingame (fullscreen, EQUAP)