The two measurements sample different atmospheric regions and different radiative transfer geometries. An exoplanet emission spectrum probes the dayside; an exoplanet transmission spectrum probes the morning and evening limbs of the day-night terminator. Several alternatives to an exoplanet cloud deck can therefore suppress the transmission feature.
Temperature, mean molecular weight, limb chemistry, continuum opacity and the dayside temperature gradient are alternatives or degeneracies to test. In particular, the three-scale-height amplitude alone cannot establish different CO abundances between the hemispheres.