It's an "upgrade" option since it must be offered to those with mobility problems, and that's just how Amtrak's reservation system puts it. The lower levels aren't as crowded, and nobody's moving through -- in winter, it can get a bit drafty by the doors.
You don't "check in" for trains per se -- at SEA, you can print your ticket from Quick-Trak anytime (even a few minutes before boarding), and check your bags anytime that day, but you'll still have to get in line with everyone else when they're boarding. Boarding is "cattle call" style, with one great big line; just be nimble and sit closer to the platform and you'll be in line before the others.