This config based detection isn't working correctly, I have jumped into
a build environment and looked at the guestfs_config.ml files:

$ for conf in $(find libguestfs-OrYVmJ -name '*guestfs_config.ml'); do echo 
$conf; grep cpu $conf; done
libguestfs-OrYVmJ/libguestfs-1.40.2/debian/build-2/common/mlstdutils/guestfs_config.ml
let host_cpu = "x86_64"
libguestfs-OrYVmJ/libguestfs-1.40.2/debian/build-3/common/mlstdutils/guestfs_config.ml
let host_cpu = "x86_64"
libguestfs-OrYVmJ/libguestfs-1.40.2/debian/build-1/common/mlstdutils/guestfs_config.ml
let host_cpu = "x86_64"

^^ This is from a x86 host.

The same on s390x:
$ for conf in $(find . -name '*guestfs_config.ml'); do echo $conf; grep cpu 
$conf; done
./common/mlstdutils/guestfs_config.ml
let host_cpu = "x86_64"
./debian/build-2/common/mlstdutils/guestfs_config.ml
let host_cpu = "s390x"
./debian/build-3/common/mlstdutils/guestfs_config.ml
let host_cpu = "s390x"
./debian/build-1/common/mlstdutils/guestfs_config.ml
let host_cpu = "s390x"

Again matching the config:
  checking host CPU and C ABI... s390x

@Richard - any obvious next steps where to look why this might have gone
wrong?

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https://bugs.launchpad.net/bugs/1864164

Title:
  virt-customize fails with "host cpu (x86_64) and guest arch (s390x)
  are not compatible" when running on s390x host

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