Oh, no! You can remaster a Knoppix with all your changes as you prefer. Then do a "Flash disk Installation" of this remastered ISO. In this Flash disk Installation you can additional changes and they will be stored in the persistent memory. But you cannot create a new ISO of "remasterd ISO" + "persistent memory".

Why? If you for example purge GIMP and then remaster Knoppix, then GIMP isn't in the new ISO. The new ISO is not as big as before.

But if you "purge" GIMP in the Flash disk installation. then GIMP isn't really purged. It remains in the compressed filesystem KNOPPIX; only some remarks will be done in the UNIONFS to make GIMP invisible.

Now, if you try to build a new ISO using your Flash disk Installation, then there would be no benefit; all is as big as before.

That is the reason, why I prefer remastering first. I get a small ISO to burn on CD or to use for Flash disk Installation. And a small ISO boots faster than a big one.