Dear Carlo,
The reference point for the rotations and integration of the hydrodynamic moments in those papers is the intersection of the undisplaced spar centerline and the still water level (SWL).
Viscous drag on the spar was neglected in the paper by Ramachandran et al, but the ROAs presented do include the so-called “additional linear damping” in surge, sway, heave, and yaw mentioned in the first paragraph of the “CASE STUDY” section on page 3.
Yes, the "-5.E9 Nm/rad only includes the effects of the hydrostatic pressure; the restoring effect from the center of gravity is taken into account elsewhere.
Best regards,