I just got the following email from Condor Travel
" We wish to inform you that PeruRail has cancelled its baggage car service that transports tourists’ additional luggage to Aguas Calientes due to operational issues. As a result, we wish to remind everyone that PeruRail only allows one (01) carry-on baggage per passenger, and it must not exceed 5 kg. (Or 11 lbs.). Likewise, please note the Ollantaytambo and Machu Picchu Pueblo Stations do offer free luggage storage services for your passengers".
So don't count on being able to take your large bags. I don't know if this is applying to all services including the Expedition but it would be good to plan for the need to store luggage.