That wasnt a flaw, that was deliberate,
In which case it wasn't a flaw but an error.
the down peak is busier. For the up morning peak the commuter service is largely done and dusted by the time the long distance peak arrives. In the evening, it all goes together…
I commuted on the GN for 25 years. I have lost more of my life than I care to think stuck at the old K632 signal on the up slow at Woolmer Green, my train delayed by late running early morning ECML trains from Leeds or Newcastle. Just because the long distance peak is later does not mean that the first up long distance trains can't wreck the morning commuter service, or vice versa.
But the key point is that both morning peak and evening peak need to be looked at because one is not a symmetrical version of the other.
In particular, what matters is how trains queue to get into the 2 track section at Welwyn, and what happens at the other end. On the down road any queue is mainly on the fast line and not obstructing any platforms. On the up road trains queue mainly on the up slow line, quickly obstructing the platform at Knebworth, and, if the situation worsens, at Stevenage and Hitchin too. Furthermore, coming out of the two track section on the up line nearly everything is on the up fast so it takes a lot longer to recover to line speed than on the down road where the queue is spread between down fast and down slow after Woolmer Green.
Hitchin is another example of non-symmetry. Down trains for the Cambridge line can use both down fast and down slow through Hitchin, up trains can only use the up slow. This is a bottleneck that is far more significant in the morning peak than in the evening peak.
A further example of non-symmetry is Holme Fen where the 2 track section is much longer on the up road than on the down road, and at start of journey for commuter trains too. A Peterborough starter late through Holme will be late at Hitchin too and blocking trains off the Cambridge branch.
Another factor for the commuter morning peak is week night engineering work, and what happens if it over-runs. This can be critical in the Fens because of the single line sections north of Ely.
To not model that south of Grantham (including the Cambridge branch) between 0630-1030 is absolutely nuts.
The above is a more long winded way of agreeing with this.