When an air handler sits in an attic, it manufactures water. The cooling coil condenses moisture out of the air continuously during the cooling season, and that water has to be captured in a primary pan, carried away by a drain line, and caught by a secondary pan if the primary fails. Each of those is a common failure point: the drain line clogs with biological growth, the pan corrodes through, the trap dries or is missing so the line will not flow, or the secondary pan's own drain is blocked. When any of them fails, the water lands on the ceiling directly below the unit — which is exactly where the staining in this scenario is. The roof being sound is what completes the diagnosis by eliminating the other overhead water source, so the report points at the condensate system and recommends HVAC evaluation rather than roofing.