Not a dumb question at all, this comes up a lot with Amtrak.
If you book a roomette as a solo traveler, it’s yours alone. Amtrak does not pair strangers together in roomettes. You’re paying for the private space, not a bed count.
The two beds are just for flexibility if you’re traveling with someone. If you’re solo, you’ll have the whole see to yourself and no one will be added later.
So yes, you’ll be totally alone in the roomette the whole trip. Enjoy it, the Empire Builder is a great first Amtrak long distance route.