Sorry, but you *really* need to learn how to express your issues/desires more concisely. That was a mess of a post, honestly.
If I understand correctly, you want :
1) an absolutely clean version of TCL
2) a way to save incremental changes to the filesystem (and/or extensions) as different points in time, and be able to load any one of these (presumably at boot)
3) different sets of extensions to be selected by the user and loaded on boot
For the clean TCL boot, you can use the "base norestore" boot codes. As for 2 and 3, the "tce" directory that TCL restores from on boot contains a "mydata.tgz" and an "onboot" file. mydata.tgz is an archive containing various directories with files that you may have changed. onboot is a list of extensions (tcz files) that are to be loaded (guess what?) on boot.
If you want to create different "profiles" to load different extensions/files, or to use as backups, you could save each "profile" to a different tce directory, move earlier profiles to a separate directory, etc. I forget if there's a boot code for non-default mydata.tgz/onboot files (i.e. with a different name or not in the tce directory), but you can simply change the tce directory in the boot code. Depending on which bootloader you use (grub or syslinux or something), you should be able to edit boot codes on the menu for which you select an OS. This way, you can manually edit which tce directory you're loading every time you boot up your TCL install.
Hope this helped, I know I was kind of unclear on some things, =P