Indeed, the Wayback Machine is an invaluable resource, more and more so as older sites drop off the net.

But hosting, for example, multiple complete MAME ROM sets (and the existence of turnkey - albeit non-commercial - products which download them automatically) is in a completely different category from the Wayback Machine - and it would be a shame if the former was endangered by the latter.

Someone would spin up a nonprofit and buy the assets and keep it going

how would this painstaking work be performed by a decentralised entity? Human beings have agendas, I am not sure why you expect them to be machines or politically neutral. This is normally understood when one donates to a charity.