Hi Vilas,
Not sure which airline you work for. At my airline it does specify in our FOM that AP and A/THR is optional below RVSM and in addition it states that it is encouraged for us to fly with the AP and A/THR off when practical. We are encouraged to use any level of automation (FDs on, Bird or Raw data as well). Would you be hand bombing it raw data out of LGA or LAX on an RNAV Sid no.. but it is not contrary to our SOPs flying with reduced level of automation.