As you have discovered, QuickDraw GX is not installed using the Restore All Software option on the Macintosh Performa 6400 Restoration CD. Instead, you must open the several folder to find the installer for QuickDraw GX.
The path for the QuickDraw GX software is:
Performa CD -> Hard Disk Files -> Apple Extras Files -> System Software Extras (scroll down to see it) -> QuickDraw GX.
Other software in the System Software Extras folder includes; QuickDraw 3D, QuickDraw 3D extras, PowerTalk, PowerTalk Extras, Sound control Panel, and Text-to-Speech.