Okay... the cover promotions are not broken... what is broken here is the default "promotion" for Siege units. No Defensive Bonuses means exactly that... so picking Cover with a Siege (or mounted or armor or any other unit that has No Defensive Bonuses) is wasted. It completely deactivates any bonuses on defense whether it be terrain, nearby GG or other Promos. You'll get NO positive modifiers when defending with these units (Tested this with IGE when wondering why my Trebs were being one-shotted by cities with Cover II).
To correct this for my mod-in-progress, I've replaced the functionality of No Defensive Bonuses setting <NoDefensiveBonus> to false and adding <RoughDefense> of -25 to offset the 25% bonus for rough terrain. Now it effectively becomes No Defensive Bonuses From Terrain but still allows a unit to gain benefits from other promotions, fortifying, being in a fort/citadel, near a Great General, etc.
I also debated the idea of adding Defensive Penalty back in (still in game in Pedia but unused by any unit) for Siege but their lower CS compared to RCS takes that into account, I concluded.
Although I am still debating add a RangedDefenseMod to all siege equipment to protect them more from city bombardment and cowering archers forcing Mounted/Armor (and Melee/Gunpowder to a lesser extent) to do their intended jobs and overrun them.