Sorry, your code part and the links within doesn't work.

But anyway, the interesting part of the script "flash-knoppix2" starts at "If we don't already have an overlay, ask to create one"

If there already exist an overlay nothing is done, if not, Knoppix creates an overlay.

If the overlay is an overlay partition, Knoppix creates the new config file "knoppix-data.inf" with the proper content. This config file is a specific file of K. Knopper and not of the Debian pool.

How Knoppix interprets this config file during boot, you can see within the "init"-file of the minirt.gz in the function mountdata() and there starting at the line "inf) # Contain partition information ...".

Read and analyze the source code.

If you want another behaviour of Knoppix and his overlay partition you have to change these two scripts, insert your own code and remaster Knoppix.