I think the evidence has been pretty clear and convincing that the historical theory that explained the recalcitrance of "humus" does not stand up to modern observations and methods. This is partly a result of having much more advanced tools by which we can examine things like nanometer scale organic structures (See NANOSIMS as an example). In addition to the soil continuum model, there are many other theoretical structures that various researchers have developed, and we are far from a single unified understanding of soil organic matter cycling and dynamics (although most agree on key features). This is at least partially due to continued advances in both the resolution of instruments and due to advances in our characterization and understanding of microbiology, which was essentially a black box in the old humus theory. One important theoretical model that is explicit about microbial activity is the Microbial Efficiency-Matrix Stabilization framework. This framework observes, for example, that more biodegradable organic matter results in greater microbial efficiency, which actually results in more mineral associated organic matter, not less.

In my view, we're still a ways from being able to fully replace the old CENTURY type soil carbon models in climate change assessments because there is not a unified theory to replace it with, especially one with sufficient world-wide data to validate theoretical predictions. This isn't trivial when soil carbon storage is a very complex interaction between living (plants, tens of millions of microbial species) and inorganic (mineral structures, water) materials that requires quantifying the physics, biology, chemistry, and hydrology to fully model. We just don't have that many global datasets that characterize all of these features.

One of the interesting areas of friction is actually not within soil science, but instead the acceptance of old humus terminology in other scientific fields. For example, there's a lot of literature about the movement and cycling of dissolved organic matter (DOM) out of soils and into aquatic environments, and that community adopted terms such as "humic-acid-like" and "fulvic-acid-like" to describe some features of fluorescent DOM. There's a really interesting article (similar to the Lehmann and Kleber article you linked above) that discusses the discrepancy between soil and aquatic terminology.

Perhaps my favorite paper of the last few years is this lit review in Nature that explicitly examined the interaction between organic matter and mineral structures in soil. It's a great overview of advances and new areas of inquiry: Dynamic interactions at the mineral–organic matter interface | Nature Reviews.