The boot.wim from the ISO that won't integrate has folders in the boot.wim, Program Files, ProgramData, Sources, Users,Windows and a file bootmgr. The sources folder has a bunch of files, mostly DLLs.
I pulled open a Windows install ISO and see a bunch of folders in it's sources folder incuding a boot.wim and install.wim. So I guess my PE has only a single wim in it.