Can the AGS set-up program be edited to be changed?
Only by changing the engine source code.
Alternatively you may create your own setup program, which should not be really difficult if you can program user interface. The configuration is saved in a simple text format, known as INI (http://en.wikipedia.org/wiki/INI_file).
Also, there was already some discussion here: http://www.adventuregamestudio.co.uk/forums/index.php?topic=48097.0
thank you