I am still genuinely trying to understand what happened.

In your interpretation:

1) What is the motivation of the donor (Epstein)?

2) What is the motivation of the acceptor (Ito)?

If your answer is

1) Prestige

2) Money

Then that does not work: they can not reach a mutual understanding about whether Epstein is allowed tell the world he donates to the Media Lab, which can be seen by splitting up in cases:

1) if the mutual understanding is that Epstein is allowed to tell the world he donates to Media Lab : in this case Ito's motive evaporates, because he was fully aware and scared shitless of Epstein's name getting associated with the Media Lab.

2) if the mutual understanding is that Epstein can not tell the world he donates to Media Lab : in this case Epstein's motive evaporates, since it doesn't raise his prestige.

So all the authors of these articles are systematically individually either unintentionally overseeing the inconsistency, or intentionally obscuring a deeper fact.

Let's hypothesize it's for the tax deductions for the root donors (like Bill Gates etc.) instead: this too doesn't make sense, if you find a scheme for tax deductions etc by donating, why not donate directly? if for some reason the tax scheme can only work with an intermediary... why on earth select a radioactive person like Epstein?

So the tax evasion angle is misdirecting chaff too...

Consider that many of the unrecognized victim(s) of Epstein (and the buyers of his underage prostitution ring) are now adult. Consider the typical promises that were made to these girls (money, and future prospects). Many of these girls are adult women today, possibly studying, PhD studying or working. If some of the girls insist on studying some place, Epstein needs to pipe hush money, scholarship, salaries into the faculties and departments.

My interpretation is that it is hush money.

Bill Gates is not shy, he openly donates to many causes. He wrote books etc...

Before this scandal there was nothing controversial about the Media Lab, so why would he donate anonymously?

Even if he insisted to donate anonymously, why donate through Epstein? Bill Gates should be smarter than that, why are we holding Ito to a higher standard than Gates? If Ito & Co were handling the connection with Epstein with radioactive precaution, why didn't Bill Gates geiger counter crackle beyond repair?

And why on earth would Gates pay off someone else's hush money?

Suppose Gates paid hush money (or was blackmailed by) Epstein for services rendered (say in a somewhat distant past) to forward the hush money to the victim(s) at Media Lab.

That could also explain why Gates would go through Epstein: if he paid the Media Lab directly, the shorter connection towards the victim(s) might be construed as a financial acknowledgement of his involvement with the victim.

It also explains why he would go through Epstein as opposed to involving a clean person: the clean new intermediary between the Media Lab and Gates would be an extra point of failure who could leak the secret.

While it might be relatively easy for the "already-did-his-time" Epstein to find a lab or department head, and convince him with his crocodile tears to cooperate in a cloak of charity to pipe the "compensations" ( hush money, work position salary for the victim ) through the department head.

Instead we have Big Media suddenly (and suspicously) spinning stories and redirecting attention to either academic vaporware like growboxes from the Media Lab, or "billionaire circuits" naturally attracting male and female "deplorables". (which is just slutshaming all over again!)