It’s funny how memory plays games on you. I’ve just dug out all my old paperwork from when I looked into this subject and I made a mistake.
In 2005, there were 40 (forty) flights a day from London to Manchester. 19 to Heathrow, 8 to Gatwick, and the rest split between City and Stansted. There were also over 100 to Glasgow and Edinburgh combined.
This was in the days when BMI ran a full schedule in competition with BA. To be fair, it is also when WCRM was in full swing, and weekend travel times by rail were extended, typically to over 3h For Manchester. It was also before the revised security arrangement for air travel - at that time you could just turn up at the gate for domestic travel, often at 20 minutes notice. But yes, most of the passengers then were genuine London - Manchester; perhaps only 20% connecting at most.
Getting back on topic, my old paperwork includes a study I had forgotten about - Atkins did some work for the SRA between 2001-2003. This is in addition to the Greengauge 21 study, Network Rail’s new line study (and it’s separate Pre-feasibility precursor), DFTs internal work, and other less ‘official’ work done by various organisations, including one specifically looking into a London - Scotland route from the Scottish perspective. All this fed into the Government decision to initiate HS2 studies in 2009.
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not much difference if you are not on a BA flight or codeshare from LHR, though. Or if you start your comparative trip from Preston, or Wigan, or Crewe.