I just inboxed a 4545 and found 3 of the steps broken off as well! Current plan is to CA them back on. Based on your post I will also do a more thorough inspection. The box itself showed zero damage so I am assuming factory error/handling.
Regarding the presidential seal with the George Bush Library and Museum inscription, I would never have noticed but do think it's lazy on Lionel's part. This is a $530 engine and attention to detail is expected.