I think there was misunderstanding with what gets collected before the rules are executed. If you have any Local Custom Objects in the Template, then those will be executed first before the Rules can be run against them.
I think collecting the top level objects is ok for compliance, as those parts aren't really evaluated by rather provide the starting point for the Rules that use them.
I'd be more concerned if you were talking about Audits/Snapshots of entire filesystem with recursive set on, other than that you should be good.
You can run some base line testing, then add the filesystem part, and run another test for comparison, but I think you should be ok.
thanks for your feedback....
We'll keep on collecting :-)
lazar - i'm not sure about the top level behaviour - i typically use the highest level object that should be there, but i don't use top level objects like / or HLKM... so i might use /etc/ or HKLM\Software\BladeLogic.