You probably can't do single point to point return reservation, since most of the connections from the eastbound Builder are not guaranteed due to timekeeping problems, and that most definitely includes the Cardinal. I think the only trains where a connection from the eastbound Builder is allowed is the Lake Shore Limited and maybe the City of New Orleans. So you'd have to build in an overnight and use the multi-city option.
Malta is the closest station to Billings, Browning or East Glacier you'd be overshooting to the west by quite a bit. Remember, the route of the Empire Builder pretty much follows US 2 across the northern edge of the state, while Billings is down on I-90. Don't know about a rental car, though. Malta is a really small town.
CHW-MAL works on May 10. Returning on May 25 MAL-CHI works, then CHI-CHW May 27 with an overnight layover in Chicago also works using the multi-city option.