Is the amtrak tag redundant if posts are already tagged with trains and usa?
No - see @choster's answer. (The tag is presently in use for 43 Open questions.)
If no, should I tag relevant questions with all three tags, or only with amtrak — probably this implies trains and usa?
Only with amtrak (and others as appropriate). As you mentioned, amtrak already implies trains and usa. @Ankur Banerjee♦'s advice is:
use the most specific tags for the question.
This is advisable in part, because of the five tag limit per question, to leave room for other more meaningful relevant tags, such as train-stations, refunds online-resources etc.
If yes, is it technically possible to make amtrak synonymous to the combination of trains + usa?
Technically Yes, but very far from being practical or ever being implemented.