The difference you are speaking of in "Inside Passage" cruises refers to Vancouver Island. Ships departing Vancouver are inside the island and cruise a narrow passage to pass it, then continue into the Inside Passage.
Ships from Seattle normally take the route outside Vancouver Island. They are indeed exposed to rougher seas and less scenery. Usually they compensate for that by stopping at Victoria, a really nice port. Often they also go to Sitka which is a port we love.
Here it is in a nutshell:
The two times we have encountered really rough seas in Alaska have been outside Vancouver Island, and enroute to Anchorage across the Gulf of Alaska. So if seasickness is your major concern, the "classic" Vancouver roundtrip would be the best choice.