Hello Ryano,
You are correct the Tools> Model options> settings are not saved to the ntl format. There is an enhancement that has been logged for that, CAE-CR-3184: Add an option to use the Autopipe defaults file when importing NTL files.
This has already been added to the AutoPIPE V8i 9.6 to be released July-Aug 2013.
Regards,
Mike Dattilio
Bentley Technical Support Analyst
Web: http://selectservices.bentley.com/
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