CL Analysis in the SEM and (S)TEM have very different benefits and choosing the right technique is dependent on your sample.
In the SEM, the sample requires little or no preparation, and many different types of samples can be analyzed trivially. The SEM is more suited to analyzing weak CL signals due to the greater flexibility in excitation conditions (large probe currents). Also, the achievable spatial resolution is sufficient for many applications but is often limited to no better than ~10 nm (depending on the sample).
In the (S) TEM, you can combine CL with other techniques (e.g., EELS) to directly correlate the luminescence with the sample’s microstructure and composition. This correlation potentially provides better spatial resolution (e.g., 1 nm) due to the low electron scattering in thin samples with high energy electrons. However, the low scattering means that signal levels are (very) low and only a limited range of specimens are suitable for analysis in the TEM.