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The database file is the same across both platforms, you just need to choose the right path: https://github.com/ReagentX/imessage-exporter/blob/c73bc4d66...

How do I make a backup without the Cloud on Linux?

Instructions I found from Apple (https://support.apple.com/en-us/HT203977) are to use the Cloud, a Mac, or Windows +iTunes.

Maybe something like https://github.com/libimobiledevice/libimobiledevice? I'm not sure, I haven't tried to do this.

libimobiledevice definitely works for this, I've done it before.