I confirmed that its "baked in" to the soak test version of 4.0.4 that I installed by looking at the file specified by chjade84 on XDA.
Disable Volume Wake Galaxy Nexus 4.0.4 Leaked ROM - xda-developers
Navigate to /system/usr/keylayout/ with Root Explorer or such and mount as read/write.
Make a backup of tuna-gpio-keypad.kl -- just in case
Then open tuna-gpio-keypad.kl in a text editor.
You will see 3 values after all of the header text information:
key 114 VOLUME_DOWN WAKE
key 115 VOLUME_UP WAKE
key 116 POWER WAKE
Delete the "WAKE" from the buttons you wish NOT to have wake the phone.
Save the file and restart.
I haven't tried it yet but I'm thinking about it...