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Yes it can ! We did this trip last June and it was very straightforward and inexpensive...9 euros return each which as you say included the metro (and I think the buses) remember to get your tickets validated in the machine on the wall in the ticket hall before you board the train or else you may be in trouble when the inspector checks your ticket!! Neither of us spoke Italian or had travelled independently in Italy before but we found everything very easy. I got street maps off the internet before we went. We found the Thomson tour organisers very helpful for those wishing to travel independently so try and go to any 'port talks' for useful info.
The B.I.R.G. is the one for the Regional trains ("R" on the schedule on trenitalia's site) and includes buses/metro in Rome. A return ticket from Civitavecchia to the main station (Termini) in Rome, including use of buses/subways in Rome is 9E.