50ml output for a mum who latch full time is fairly good. Whatever you pump is on top of what your baby drink so I think your supply will increase after some time. The time of the day which you pump will also affect the output. you should see more vol in the morning. Just remember at least one month before you start work try to pump as per your pumping timing in thd office and get someone to help bottle feed. It will help you decide whether there is a need to change your pumping schedule. Usually it will take some time for your body to adjust to pumping.
As for flange size make sure your nipples are not rubbing against the funnel. If so you need to change to a bigger flange. If too much aerola is drawn in you need to change to a smaller size. Pumping should not hurt.