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Are you referring to the 6.5 Best Practices Doc?
Regardless, I think the reference is about leaving the port selection set to the defaults. There is no option to "Allow Foundstone to determine which ports to scan".
If you have a 6.8 best practices Guide, let me know. I've not seen one since 6.5. I can recommend the author remove that specific reference.
Im refering FS 6.8 Best Practices as stated in my previous post.
What "Allow Foundstone to determine which ports to scan" is referring to the default port list as Cathy stated.
Basically how this works is that if you select a script that targets a port that is not in the default port list it will be automatically added to the scan configuration. This allows the port list to become dynamic based on what types of checks you are running.