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.Read less <