If you want to "Force" Settings, just modify the client.cfg to add your custom config.
.include "login.cfg"
.include "test.cfg"
.include "preload.cfg"
.include "options.cfg"
.include "user.cfg"
.include "forced.cfg"
Then create the file "forced.cfg" and add whatever settings you want to it, this way nothing can alter your forced settings. (Set it to readonly too if you want as it wont mess up your other settings).
Example: you define your resolution in the forced.cfg, even though you change resolution with the SwgClientSetup_r.exe, the forced config gets loaded last so the client reads your forced settings.
Just put the following in your forced cfg.
[SwgClient]
allowMultipleInstances=true