You cannot,that's imperfect of IP awhile.
Not true.
It comes down to whether or not the package in question has those icons. If it doesn't, they'll just remain the default Windows icons. IconPackager can indeed change the icons of all of the icons he has shown in those images. A lot of the older Icon Packages were made for Windows XP, which didn't have many of the library icons used by Windows 7 or 8. Using those old packages will obviously result in many missing 7/8-specific icons.
As for IconPackager as a whole, a lot of it comes down to how Windows has the icons set up, not how Icon Packager deals with them. I'm not sure why some of the icons in the Control Panel can't be changed when they're able to be changed manually, but there are a lot of icons in use in a lot of places that are tied to various system files and packaged like sprites. For instance, there's a little shield icon used all over the place in Windows 7 including the main page of the Control Panel, which is controlled by the shell32.dll. Icon Packager can't change this, because shell32.dll is always running as soon as you log into Windows. If you try to swap out that file, it usually gives you a warning. There are some really hacky ways of changing this file, but the most efficient way I've found is to log into my Ubuntu installation, mount my Windows drive, and then swap files.
Other annoying icons that use shell32.dll are displayed in places like the Windows 7 Explorer Command Bars...
It would be really great if IconPackager allowed you to change shell32.dll. Though that would require it to run a process on boot that replaces shell32.dll before Windows loads that file, and Stardock's employees are either unwilling or incapable of writing that script.