Currently the prepare_linux_cross() function in cue.py can only edit configure/os/CONFIG_SITE_ files where the host architecture is linux-x86_64. It should use the host-arch it's running on to allow cross-compiling from other host-arch's.
Not sure whether any other changes will also be needed to cross-compile from other host-arch's.
See epics-base/epics-base#675 for Jerzy's attempt to build for Linux on a Mac.