I'm confused. Are you saying that the IA should run the Wayback Machine and library under one entity, or two different entities? In your reply to JumpCrisscross, you seem to argue for one, and that two would have no benefit; but your link contradicts that.
Your link is about substantive consolidation, a process where the bankruptcy court combines multiple related legal entities into one. This can benefit the creditors of Entity A, since it may frustrate the debtor's attempt to shield assets by placing them in a related Entity B. Your link correctly notes that a nonprofit can't be forced into bankruptcy, and thus can't be forced into substantive consolidation. So if the IA used the two-entity strategy, then your link implies it would be quite effective--worst case, the publishers take all the assets of the library entity, and they have no way to touch the Wayback entity.
If both the Wayback Machine and the library are under the same entity, then that single entity still can't be forced into bankruptcy, because it's a nonprofit. But the creditor (i.e., the publishers with their hypothetical judgment) can still just collect against the single nonprofit entity, bankruptcy or no bankruptcy. If the judgment is for more than the entity's assets then the creditor gets everything.
The point of bankruptcy is to consolidate multiple creditors' claims into a single case, to be resolved more fairly, while destroying less value, etc. It seems like you might be thinking that no bankruptcy means no ability for the creditors to collect? But that's exactly backwards--bankruptcy is primarily a set of protections for the debtor (like the "automatic stay", which stops creditors from trying to collect outside the bankruptcy), with a few smaller benefits for the creditor (like that substantive consolidation) thrown in.
ETA: And I see that the IA describes itself as "recognized as a library by the government", but I'm not aware of any specific legal benefit from that. Regardless, if that's somehow important then they could leave the books in the library entity and split out the Wayback, instead of splitting out the library.