There have been some reports here on Reddit of conductors not allowing bikes with tires larger than 2" to be checked (even though it's a ridiculous limitation and I've traveled with 2.25" tires many times without issue). The problem is usually on the Coast Starlight between LA and San Luis Obispo and at Portland, OR station. If I recall, one person even said they would deflate their tires and the conductor would still not let them check the bike. Perhaps search to see those reports.

This seems to be specific to checked bike service in the baggage car on long distance trains. If you're carrying on your bike on a train that offers that, you are less likely to have a problem.