The second paper is available as Phys. Scr. 79 (2009) 065013 (29pp). An editor and a referee or two think there are not too many things wrong with it, or that it has enough good things about it. One assumes Luboš was not a referee. The whole community doesn't vote on whether a paper is accepted into a journal, of course, so a pinch of salt, but as of now there are 26 citations to the 2009 paper in published papers, according to Web of Science (which is not shabby at all). The editor required them to cut down the paper significantly, 64pp→29pp, so one of the worst;-) things about the arXiv version is mitigated in the published paper.
I take this kind of approach to QM to be on the edge of engineering and interpretation. There is an engineering problem that is addressed by tomography — how do we determine what quantum observables we are measuring (and the relationships between them, expressed in terms of the mathematical ansatz we use to model them) and what quantum state we have prepared, from the basic classical raw data points (that are written in lab note books or stored in computer memory) and whatever statistics of that raw data we may construct? Note that the engineering problem begins with classical information and ends with quantum observables and a quantum state, and, as such, is intimately concerned with the interpretation of QM, at least in the old-fashioned vaguely formulated terms of the Copenhagen and Bohr's interpretations. For more modern interpretations, which often layer some kind of metaphysics of the quantum state on top of the raw data, the relevance is not as clear-cut.
The worst thing about the second paper may not be something for which it can be hung out to dry, just because no one else has achieved definitude: it does not construct a compelling account. Specifically, it does not compel Luboš to take it seriously. This is an extraordinarily difficult balance to achieve, however it looks to me that if current progress is maintained someone will find an adequate combination of simplicity and mathematical and philosophical sophistication in the next 10 years.
Having written part of this before Roy Simpson's Answer, I have up-voted his Answer and commend it to other people as a counterpoint to the approach I have taken. I commend the papers cited in the Question as useful for engineering purposes and as a valiant attempt at interpretation.