Adding to earlier replies it’s also to do with the typical expected usage for the trains being maybe a maximum of 20 hours of a day, say about 0530 off a depot, that would mean a return to usually a different location by around 0130 the next morning. Compare that approx 20 hours normal use with the Aberdeen to Penzance time of around 14 hours. So your spare time for the two unit proposal is about 6 hours each. If that was done over the whole XC network it means the train fleet would be getting towards possibly 30-40% too large. Ideally that 6 hours should also be productive time, but only if there are sufficient or suitable passenger flows to justify it. So as others have said it runs empty from Edinburgh to Dundee then in service Dundee to Aberdeen. That latter service might possibly be useful to fill a gap or add capacity in the local Scotrail service pattern at that time of day. I suppose if Aberdeen and Penzance were only a few hours further apart, say 17 hours, a two train service might be feasible, but they’d still need swapping out for major maintenance.
Unfortunately if there aren’t suitable overnight depots at both the extreme ends of the route, something has to flex. If there was a suitable overnight maintenance depot at Aberdeen it would be more likely to have a northbound train ending it’s day there, having started out with a short trip into Penzance.