Mako uses "runtime" internally for things, and if you clobber it stuff will just break in weird ways. So don't do that.
make sure the arch templates (s390 excluded) copy the runtime image in to the /images/ dir, and make sure it gets grafted/copied into the boot.iso.
TreeBuilder uses templates full of commands (like ramdisk.ltmpl) to create the output tree and boot images. There are 4 arch-specific templates, plus a bonus EFI template which can handle EFI image creation for any arch that implements EFI.