Operating a machine includes supplying electric power from a fuel cell to a power bus connected to an electric motor and an energy storage device in a machine operated at a work site, and determining an expected efficiency gain condition based on at least one of terrain data of the work site or machine activity data of the machine. Operating a machine further includes prognostically limiting a power output of the fuel cell based on the determining an expected efficiency gain condition, and charging the energy storage device during occurrence of the expected efficiency gain condition using at least one of a regenerative energy device or the fuel cell. The energy storage device may be discharged during prognostically limiting a power output of the fuel cell so as to share a load demand of the power bus between the fuel cell and the energy storage device. Related apparatus and control logic is also disclosed.