I was refreshing the bug after a debug session and found your hint to
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=946594#46

We have a new in proposed that merges libguestfs/1:1.40.2-3 (and later).
Let me try the version from proposed ...

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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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