Just wanted to confirm whether we would need to restore
to ensure all available sites were enabled
for any custom email routing?
The only reason I can think of for not restoring these directories would be if ISPConfig automagically re-writes any missing configuration files. But these directories are not mentioned in any posts I have read about backing up or restoring.
The script posted by go0ogl3
backs up the entire /etc directory - which is clearly intended to be restored to the same server.
So perhaps it would be useful to confirm the list above as the minimum requirement to migrate data from one server to another.