I strongly disagree, having dealt first-hand with the fallout of identity fraud. These escape hatches negate the purpose of names. The problem with storing "legal" names is the custodial burden of storing any personally identifying information; however, the benefit of dealing with a bona fide person may outweigh the cost.
In the case of an academic institution, it is completely reasonable to use a legal name as the standard. If a person doesn't like their name, then the onus today is on them to change it. This article doesn't propose any constructive alternative, that maintains the integrity of the academic system which is relied upon, in an important way, for things like visas, scholarships, and employment.
The preachy disagreeable manner that this article was written in doesn't help. The appeal to collective cause indicates a defective and illogical mode of thinking. The argument as presented lacks a logical basis, instead trying to appeal to emotion through example and anecdote. Who is this person, to dictate my duty? And furthermore to decide the meaning of basic terms, such as what a name is?
No thanks.