We've taken the AutoTrain many times with both car and motorcycles, however I can't remember if they even do "checked baggage" since you typically leave all your belongings other than a carry-on bag in your vehicle. If traveling by car, I'm not sure this would be a problem declaring and leaving your firearms in locked cases in a locked trunk. The 'drivers' loading cars onto the train are in such a hurry and under time pressure to get loaded, there'd be little time to search for and find your weapons. In the case of motorcycles, especially like ours with 'soft' saddlebags, I'm not sure I'd be comfortable leaving my weapons in the saddlebags.
My suggestion would be to contact Amtrack and get answers IN WRITING, then figure out whether you want to take and secure your weapons, then have copies of that correspondence with you when you travel to show you've complied with what you have been told by Amtrack. Remember... the typical LEO will not know the intricacies of their own State firearms laws, and will have even less knowledge of Amtrack's regulations or policies. They will likely... arrest first, read the law later!