Can you have a single active instance in a GigaStor and capture packets on a subset of ports and then have network trending/metadata on all the ports?

Yes. Create a filter for just those ports as a Software Filter. Apply the Software Filter (make sure you are not doing a Hardware Filter) then in Trending, go to Settings and select the option for Use Current Filter. When you click on OK, you should see the name of the applied filter on the Network Trending screen.