LVDS connection via HSMC connector on Cyclone III Starter Kit

They must have written the comment for a reason. It isn't likely that someone with firsthand experience will reply due to the age of the board. If you want to roll the dice, go ahead and atleast create a dummy project with pin assignments and constraints for what you are planning and see if there is some subtle rule preventing it from ever working. Otherwise, I would say pick a newer board that doesn't have such constraints like maybe Be Micro ones.