Here's how well this experiment went for me:

Note, for perspective here, to reconstruct my favorite LiveCD from my
...Changelog notes 'by hand': 'ALL' manual changes might take hours;
...'All' manual changes: 10's of minutes; 'all' changes: just minutes.

GUI Software manipulations:
IceWeasel works, ALL changes retained; includes
...HomePage def'n, add-ons & deles, mail, passwords, bookmarks, history.
LXDE & PCManFM work, ALL changes retained; includes
...Desktop redefinition & tweaks to PCManFM.
Synaptic works, All changes retained; amounts to
...de->us repos, 2 programs removed, 2 added.
Network Manager & Broadcom wifi, All changes retained; includes
...SSID, WEP key, keyring password, Broadcom wl driver.
Compiz works, all changes retained.
LibreOffice spreadsheet works, all changes retained.

Command line tweaks:
Alsamixer, all edits retained
/etc/X11/Xsession, all edits retained.
/etc/syslog-knoppix.conf, all edits retained
/mnt-system/boot/syslinux/syslinux.cfg,' all edits LOST
...the ONLY item not transferred, since /mnt-system is not in KNOPPIX-DATA.

Here's how the two LiveUSB's compare:

Each goes from start-of-boot to on-line-with-wifi in 1m45s.
Each is 244 Mb smart in knoppix-data.img. Actually most of this 244 Mb
...is for an empty but necessary filesystem, and the bare essential files
...therein which any system needs to operate.