Err, that's for manipulating ROMs, which he reverse-engineered the format of. This is useful when you want to add or remove programs (i.e. for deployment in a company).
If you want Windows CE (WM5) on the Zaurus, grab the Platform DDK (or something like that) from MS, which is a free 30-day demo (several thousand after that). A much cleaner and easier solution than trying to modify and cram a device-specific build of WM5 from another device onto a Z.