Central to the whole story and integral to it is the destruction of Data.
When I tried to renew my son passport in 2012, the passport office put a temporary stop for more details on his application (the downside of a father applying apparently). When I called in, as a part of the "lovely" discussion with the Passport Office clerk I was told that all original documents serving as a basis for permanent leave to remain and any citizenship resulting from it have been destroyed. Deliberately. This is what we all know now to be the process of destroying the Windrush Landing Cards. It was not just the landing cards. It looks like quite a few other things were destroyed at the same time - work permit files, grants of permanent leave to remain, citizenship paperwork, etc.
So first and foremost, an integral part of this story is the fact that the home office chose (and quite deliberately) to destroy all "legally binding" primary original data in its possession and try to run the process off correlated hearsay being collected by other agencies.
That started the clusterf*ck. What the article describes is just the later stages and the conclusion of it. It was when the home office was trying to close the barn AFTER the horse had bolted. The NAO never got anywhere near the original decision which was frankly at the root of a lot of the Windrush (and later) clusterf*ck.
We still do not know who signed that order by the way. According to some of the posts on the subject on previous el reg articles it actually was in the days of Bliar, predating the Treasonous May.