Yes, you can 'prevent' overwriting existing Dynamic System Settings. However, this only works when you import rules manually. During the import you have the option to exclude aged updates. When these settings are newer on the target system, they get marked for aged updates.
However, currently this ONLY works for manual imports. If you use the PRPCserviceUtils to import, aged updates always be overwritten. In my opinion this is a bug.
If 'included associated data' is checked in your product rule, you might consider removing the ruleset association on specific instances. This way you will exclude these specific instances from packaging.