According to Sebastian's further analysis of the problem (thanks!) I think this simply cannot be completly solved in an automated way. I'd suggest that this bug is solved by adding a bit more text to line 122 in fai-setup, stating that the user may need to edit $sshdir/known_hosts if the server may be contacted via further names. Then this bug could be closed properly, otherwise it should be tagged wontfix.
Best, Michael
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