A maximum power point tracker is a solid state device that exposes the PV array to the DC voltage that maximizes its power output. HOMER assumes that the PV array is being controlled by an MPPT because in most cases it is, and because modeling a system that lacks an MPPT is more complex and much slower.
The ‘tracking system’ that appears on HOMER’s PV Inputs window refers to a mechanical system that orients the array towards the sun to maximize the incident solar radiation. The default tracking system is no tracking system at all, since most PV arrays have a fixed orientation. But HOMER can model various one- and two-axis tracking systems.