The base system used depends on the installation, though normal references via cockpit instruments are by magnetic north.
For example, the 744 has no magnetic compasses other than the standby compass. The FMS derives courses and headings from the IRUs, which are referenced to True North, plus computed Magnetic Variation. The computed Magnetic Headings/Courses are then displayed in the cockpit.
True Headings/Courses are displayed in the Polar regions or when selected by the pilot.