Fundamental Instrumentation Feature Guidelines can be found in the following article:

What is the best reporter for both in vivo and in vitro optical imaging?

The luciferase signal produced by transfected cells is too weak to be detect by Flow cytometry.  The cell would need to be immobilized in order to detect signal which defeats the purpose of flow cytometry.  Traditionally, cells emit between 10 and 1000 photons/sec.  With fluorescence this is in > 1M ph/s.  Most researchers will look into dual reporters with a luciferase for in vivo imaging and a fluorescent protein for in vitro purposes. A good reference is:

A few rules of thumb apply to choosing reporters for deep tissue in vivo imaging. Tissue is a turbid medium which absorbs and scatters light. The double bonds in the hemoglobin molecule structure significantly quench light <600nm (*). Therefore one preferentially chooses a reporter that emits >600nm. For fluorescence imaging we need an excitation light source to provide energy for subsequent light emission.