This isn't about keeping public information entirely secret. It's about controlling where and how public information is shared. As an individual, you might agree to have your telephone number and your address published in a paper telephone directory, but you might not be so keen to have that information published in an easily scraped online service leaving you with obnoxious sales calls, and junk mail.
The same applies to a non-profit as well.
> the information of the org is a matter of public knowledge
Yes. But the what and the how is typically explicitly outlined by local laws.
Typically, you could direct yourself to a local tax office or public registry where you could search and look into basic information about a legal entity as defined / outlined in a legal statute.
You might find that domain names aren't required to be divulged publicly by law, and doing so is entirely at the discretion of the organization. (Example in the same vain: a public office isn't going to outright hand you a list of employees at a company if it's not legally mandated)
Whether there's a moral responsibility is a different question.
> These issues are critical for the trust that the libera.chat domain isn't suddenly going to be pointing elsewhere due to it not being control by the "trusted" org.
The freenode.net domain name isn't pointing to anywhere differently over the past period. It's also still very much registered to Freenode Ltd. That hasn't changed. What really changed is the control over the Ltd as the a majority stake in voting rights changed hands some time ago, and how that majority stake is now suddenly behaving very differently.
In that regard, DNS records aren't a definitive indicator for trust.
You have to amend that by (a) looking at who's represented in the board governing the non-profit, (b) look at documents such as yearly account balances and year reports which are typically legally mandated to be made publicly each year to see how the organisation is governed and (c) gauging day-to-day operations.
Last week, I made a remark that the libera.chat website was precariously terse in contact information or mentions about it's legal status or whoever was behind this initiative. It's assuring to see that the website has been amended over the past week with the "bylaws" section and the "about Libera" section with mentioning full composition of the board as well as whoever actively contributes to the organiation.