What is going on, I think, is that a slightly more "advanced" form of remastering is done, where the cloop images are created subject to the 4GB filesize constraint. The overlays are collapsed, but two non-overlapping images are created. If your files are to reside on less restricted file systems, you don't need to care about that - unless there is some limits in cloop file creation. I mostly use a "knoppified" version of plain Debian now, and there squashfs is used. But the principle for remastering is exactly the same.
I think you should not let the lack of updated scripts stop you. There are several code snippets posted here through the years to work from.