I just did a full wipe and installed Hybrid RC1.1 and set out to try the tool and see if it worked. After using the tool and rebooted as instructed I used root explorer to change the permissions of the newly placed init.d folder in /system/etc to rwxr-xr-x then I supercharged my phone with V6 Supercharger which placed the 99Supercharger file into the init.d folder as opposed to /sdcard/V6_SuperCharger. Did the superclean and restart. To verify that the init.d injection worked, after reboot I used script manager to run the 99supercharger script located in /sdcard/V6_SuperCharger that I would have previously set to run on boot with script manager before using the tool and lo and behold the script returned that my system was already supercharged.
So are there you go, I believe I can confirm with DaGr8's Hybrid RC1.1. If this helped you out make sure to go thank puppet13th for the tool.