Possible solutions
1. Post-install script. This is common if you are a large Enterprise admin,
your task is to push installations to multiple targets using a common
install source but of course each target must have certain unique configs
like machine name, mac address, pre-configured user access, applications,
etc. A Hosts file can be pushed or pulled similarly.

2. Depending on your distro, there may be tools to modify the install image
itself that are easy to use. So, for instance on openSUSE you have kiwi and
SUSE Studio.

3. You can mount a bootstrap image(partially installed image of final
deployment), eg regular mount, as a loop or as an NFS mount or as a chroot,
then copy the Hosts file to it, then copy the files to the target.

All seem to me are possible options. I don't know why you should think an
unsupported file system should be an issue if you're using a typical
virtualization technology like QEMU(there are also others) that supports
virtualized file systems. Would be a problem only if using something like
chroot or LXE which unlike full virtualization run as Host system processes
and use the Host subsystems directly.

So, for instance in one scenario you might want to experiment with an
unsupported file system on Linux. So, if FreeBSD supports that file system,
then create a FreeBSD Guest on that alien file system using something like
QEMU on your Linux box.

Tony

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