Great question! The overall answer is: it depends.
I’ve seen Guilds take many forms in Agile (capital A) organizations and I’ve personally created many flavors depending on the type and needs of the organization. The structure we used at Yodle/Web.com did resemble some of the structures you asked about, such as matrix organizations. I think that the major difference is that Guilds are synonymous with teams that use Agile processes. They tie in tightly to agile principles and contribute to the idea of a multidisciplinary team (T-shaped skills) that is self organizing and autonomous. Guilds are a way of making sure that these autonomous teams are also successfully operating in an environment where organization wide missions and standards can still be achieved with consistency.
As far as Mintzenberg’s species go, this type of structure promotes a Project Organization. The idea is to align and empower to have people closest to the problem solve the problem.
I agree that HR can have trouble dealing with fluid systems, but it is certainly not impossible. I’ve been lucky enough to work at several companies with this type of fluid structure and it requires buy-in from executive management and from People/HR teams. Most successful tech startups I know have achieved some measure of success with a structure that is more fluid because it allows the organization to adapt to changes quickly. This has often been developed out of necessity and gives them a significant advantage over more bureaucratically structured companies.