  In recent years it has become common practice to divide observed transit
absorption spectra by synthetic absorption spectra computed for the transit of
an atmosphere-less planet. This action supposedly corrects the observed
absorption spectrum, leaving the sole atmospheric absorption signature free
from the biases induced by stellar rotation and centre-to-limb variations. We
aim to show that while this practice is beneficial, it does not completely
correct the absorption spectrum from the stellar distortions and that some
residual biases remain, leaving a possibly altered atmospheric signature. By
reducing the problem to its most basic form, we show that dividing the observed
absorption spectrum by a synthetic absorption spectrum of the planet does not
isolate the pure atmospheric absorption signature. We also used simulated
synthetic transit observations to assess the magnitude of these residual biases
in typical transit observations. We show that dividing the observed absorption
spectrum by the planetary absorption spectrum results in an atmospheric
signature modulated by the ratio of the flux behind the atmosphere and the flux
behind the planet. Depending on the non-homogeneity of the stellar spectrum,
this leads to distorted atmospheric signatures. Eventually, directly analysing
these biased signatures will lead to wrong estimates of planetary atmosphere
properties.
