ABSTRACT In a companion paper, we introduced a publicly available pipeline to characterize exoplanet atmospheres through high-resolution spectroscopy. In this paper, we use this pipeline to study the biases and degeneracies that arise in atmospheric characterization 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 multispecies 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.