My only quibble is with your terminology, but yes. In my mind (and I think in Amtrak's mind), you get points for your fare and room. There is no "half of the fare" for the rail charge; there are two rail fares. The ticket price (if this is a single leg journey) comprises two rail fares and an accommodation charge. As I said, it's a quibble over phrasing and the result is as I understand your description.

Amtrak has occasionally listed my companion first on the ticket, and therefore my companion got the points for the room. If this happens to you and your spouse does not have an AGR account, then the room points go to waste. One time, I called AGR and asked that the order of the names be reversed and the agent told me it couldn't be done. I believe, with no evidence, that the agent was ignorant, but I didn't press the issue because my companion had an account. If this ever happens to you, I would suggest pressing the issue until the names do get reversed or simply getting an account for your spouse. I've never done it, but there is some way to refer someone for an account and then get extra points for the referral, perhaps on both accounts.