I agree that it is maddening. The same thing happens when purchasing hardware. Companies that do B2B transactions don't always support billing to myriad small entities within a single-named organization with a single purchasing department.

There are ways in which it makes sense. The company generally wants to interact with a legal entity, not a research group.

A hybrid approach, that happens occasionally at the University of Washington, is that a department negotiates a discounted license for a software license and then opens the license agreement to broader swaths of the university.