These top 10 flow figures are extracted from Network Rail WCML Route Utilisation Study of July 2011 (and previous) and it states that they are based as LENNON ticket sales database figures.I did say a lot, not all, of the Virgin services leaving Manchester in the evening peak are carrying more local commuters, than London passengers and did also point out that long distance travel is much higher on Friday evenings than on other days of the week.
For which they are no paths to do. If they used Voyagers for other London services it would make more sense to do what some of the open-access operators are proposing and do Blackpool-Euston or Huddersfield-Stockport-Euston. The former would allow some of the commuter traffic to move off the Glasgow services and the latter could mean some of the busier Manchester-London services could omit Stockport.
Remember those are total figures. On some morning Manchester-London services there are more people waiting to board at Stockport than they are already on the Pendolino arriving from Manchester. Obviously, that doesn't apply all day.
I also imagine those figures involve some guess work. If I buy a Bolton to London ticket it's probably assumed that I board the Virgin service at Manchester Piccadilly, when I could in fact go via Wigan or change at Stockport.
I don't know if they are recording point to point sales over the core route sector only (eg Euston-Manchester or v.v) or whether trips with an origin or destination elsewhere (eg Euston - Bolton, Euston-Rochdale, Manchester - Ramsgate etc..) that would involve making a connection onto or off of the core route are also included in the total figures or are counted separately.
You are correct in saying that where a connecting service is involved and a passenger is travelling with a walk on fare, assumptions have to be made about which route they will take where there are various alternatives, which is the type of calculation built into the ORCATS system for revenue allocation.