All raspi-config does is editing a few configuration files, which you can also edit with a script. Check the sed manual to see how such edits can be efficiently done.
If you have a lot of changes to apply in this way, I would consider setting up a clean RPi image the way you want, diff its complete filesystem* against a vanilla image, and then apply the changes with patch when you need to set up a new installation.
Finally, take a look at tools such as etckeeper - those are specifically designed to manipulate configuration changes and are able to track subtle changes a simple diff would miss, such as permissions. Note that contrary to its name, etckeeper is not restricted to /etc, e.g. running etckeeper -d /boot init; etckeeper -d /boot commit will make a backup of the files in /boot.
(*) Apparently it isn't obvious, so to clear all misunderstandings, I mean you should run something like diff -r /etc /mnt/vanilla_root/etc > etc.diff and diff -r /boot /mnt/vanilla_boot > boot.diff, not diff my.img vanilla.img.
/usr/bin, if that helps. If you want to disable it starting up with a fresh images, delete/etc/init.d/apply_noobs_os_configand the link in/etc/rc2.d. – goldilocks Mar 22 '15 at 13:34