  In a companion paper, we introduced a publicly-available pipeline to
characterise exoplanet atmospheres through high-resolution spectroscopy. In
this paper, we use this pipeline to study the biases and degeneracies that
arise in atmospheric characterisation of exoplanets in near-infrared
ground-based transmission spectroscopy. We inject synthetic planetary transits
into sequences of SPIRou spectra of the well known M dwarf star Gl 15 A, and
study the effects of different assumptions on the retrieval. We focus on (i)
mass and radius uncertainties, (ii) non isothermal vertical profiles and (iii)
identification and retrieval of multiple species. We show that the
uncertainties on mass and radius should be accounted for in retrievals and that
depth-dependent temperature information can be derived from high-resolution
transmission spectroscopy data. Finally, we discuss the impact of selecting
wavelength orders in the retrieval and the issues that arise when trying to
identify a single species in a multi-species atmospheric model. This analysis
allows us to understand better the results obtained through transmission
spectroscopy and their limitations in preparation to the analysis of actual
SPIRou data.
