Heathrow-Manchester is all the way down to about 7 a day now, and if Easyjet ran flights from Stansted they've already gone. Flybe tried Southend as well, that didn't last either. Like you say the passengers are most!y connecting at Heathrow and are unlikely to be persuaded by HS2. Leeds is an even better example of this - the frequency there is such that absolutely no one would think to use it for travel between London and Leeds, but some flights do still exist. The only way to get rid of flights between the North and London is probably to ban them, but that could be done now, HS2 won't make that much difference. A ban on flights to Scotland would still be unpopular in Scotland even after HS2 given journey times will still be substantially longer.
How the CO2 emissions stack up for Heathrow vs Amsterdam etc depends where the destination is - people from Scotland or northern England are already extending their journey in going via Heathrow.
Something that the review would have considered is how likely the 1 million passengers switching from air travel to HS2. This equates to about 13% of London/airports which would most benefit from HS2 services.
Now many of those are to the Central Belt, which may only see that, however others, like Leeds London may see all passengers switch.
As between Leeds and London passenger numbers were 103,706 (average of ~290 a day) in 2018 however in 2017 that figure was 162,042 so has seen a significant drop in passenger numbers.
Looking at the monthly figures 2019 may recover some of those losses (as some months are up a little whilst a few are down a little) but not all of the losses seen and probably not by a long way.
If you were to build HS2 then it's likely that you would see those numbers fall further.
As I've said before there must come a point where a landing slot at Heathrow would be more profitable to switch to being used to fly somewhere else over being a connection for travel between domestic and international flights.
Now whilst these are still fairly full (145 passengers each way, so just over 70% full on an aircraft with 200 seats) they will continue to be viable. However I'd suggest that it wouldn't take much for that landing slot to be more profitable being used for something else.
Especially given that those from Leeds can't connect with morning flights out of Heathrow or with afternoon flights in to Heathrow without an overnight stay. In comparison to the 13:55 arrival time at Heathrow from Leeds you can arrive by train by 10am, even allowing for 3 hours for check-in and a delay in your train that's still the ability to get a flight an hour before you otherwise could.
Heading the other way the flight leaves Heathrow at 11am so unless you're flying overnight and landing fairly early that's another overnight stay, whilst by rail you can leave Heathrow to until 6pm and still be home by 10pm, which would give you many more flights to pick from.
Shorten that journey time (potentially to closer to 2 hours, with 1.5 hours Leeds - London and 30 minutes London - Heathrow, using Crossrail, which doesn't even account for changing at Old Oak Common) and simplify the trip so only one change and it's likely to make air very much less attractive.
If that then means that few would choice to fly and take the train instead, it's then less likely that the route would remain.
Repeat that across Manchester, Newcastle and the Central Belt and it's easy to see how you could exceed the 1 million passengers expected to switch from air to HS2.
If the review concluded that there's scope for more of a shift from air (which could be the case) and so the assessment is accurate.
That's part of the point of the review, to see if the assessment is correct. There may be complaints that there's not much of a shift from air to HS2 (1% of HS2 passengers), but that's not what's being looked at.
Unless people can show that the assessment is wrong then the review is unlikely to be that interested.