Ok, here's some extremely current info, since I'm posting from the Silver Star in northern Florida, having just eaten the Flatiron Steak
First, there's no asterisk, star, or footnote on the current menu about beef entrée substitutions. Single asterisk is about alcohol and appetizer not being included for sleeper class passengers. Double asterisk is the FDA warning about rare steak. I can't speak for menus before Friday, or in the near future, but right now there's no such note.
Second, my server (an excellent 20-year veteran adept at carefully serving coffee over some of CSX's worst track) said steaks would be changing in June. They'll still be Flatiron, same caterer, but Amtrak has requested that the caterer do some pre-cooking to the steaks. This is temporary, just for the summer. The reason is that most people order steaks medium to well, and cooking them all that way takes a lot of time; they don't feel like they can handle that amount of cooking time per steak with only one chef during peak season. Steaks will still be "cooked to order" on board; but unfortunately, for lovers of rare steak, this means we may be out of luck for a few months. Nobody else should notice a difference. Again, this is a temporary measure for peak season, starting within the next month and probably lasting three or four months, according to my server.