If the FMS uses the usual Honeywell algorithms, then temperature isn't a factor. The FMS plans step climbs and optimum altitudes based on Cost Indices and entered winds only. The reason for ignoring temperature is that it is in effect irrelevent in calculating the altitude for best Specific fuel Consumption (which is really all it is doing). As OAT increases, so does Fuel Flow, but also so does TAS, so the calculation of NAM/Kg Fuel remains constant for any given weight, regardless of OAT.
All clever stuff, but these FMS programs are not really that clever, it's just that they save us having to look up reams of tables in a book.