PAMELA and, more recently, AMS-02, are ushering us into a new era of greatly reduced statistical uncertainties in experimental measurements of cosmic-ray fluxes. In particular, new determinations of traditional diagnostic tools such as the boron-to-carbon ratio (B/C) are expected to significantly reduce errors on cosmic-ray diffusion parameters, with important implications for astroparticle physics, ranging from inferring primary source spectra to indirect dark matter searches. It is timely to stress, however, that the conclusions obtained crucially depend on the framework in which the data are interpreted as well as from some nuclear input parameters. We aim at assessing the theoretical uncertainties affecting the outcome, with models as simple as possible while still retaining the key dependencies. We compare different semi-analytical, two-zone model descriptions of cosmic-ray transport in the Galaxy. We test for the effect of a primary source contamination in the boron flux by parametrically altering its flux, as well as for nuclear cross section uncertainties. Our study on preliminary results from AMS-02 suggests that, differently for instance from the leptonic case, realistic modelling of the geometry of the Galaxy and of the source distribution are of minor importance to correctly reproduce B/C data at high energies and thus, to a large extent, for the extraction of diffusion parameters. The Ansatz on the lack of primary injection of boron represents the most serious bias, and requires multi-messenger studies to be addressed. If this uncertainty could be lifted, nuclear uncertainties would still represent a serious concern, which degrade the systematic error on the inferred parameters to the 20% level, or three times the estimated experimental sensitivity. In order to reduce this, a new nuclear cross section measurement campaign is probably required.
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