Not the whole season but I think they have to do more than one at a time. Shooting on location costs a lot of money. Plus there is the scheduling issues with the guest stars. Also Amell is in too many scenes in both present and flashback scenes for both to be shot second unit at the same time.
Who knows for sure though. Its going to be fascinating to learn on the DVDs how they planned all that. Not just in the filming but writing too.