Re: This is not journalism
There are myriad misstatements in the article (journalistic standards aside). An LLC is not "incorporated'" no matter in which state it is formed (or domiciled). As for comments, not "many" but "the majority" of US entities are formed in Delaware, specifically for the favorable disclosure laws there (reportedly, over 2/3 of Fortune 500 Companies are Delaware entities).
Indeed, for large transactions, multiple entities are usually involved. Whether I like or dislike the supposed secrecy of the details of the deal is not my concern. Nobody is holding a gun to any non-profit's (or for-profit's) management to maintain a .org domain. If the price gets too high, switch to something else. It's not 1995, and the TLD is nowhere near as important as it once was.
Just my couple of bits as an IT consultant, practicing accountant (Enrolled Agent), and board member of a 501(c)3 organization with a registered .org domain.