Personally, I feel 2. is justified to be considered bug, or oversight. After all, one such issue is indeed fixed in patch (set up artillery). Other "may" follow in future patches.
3. is tricky, since for example riflemen get big boost if upgraded from pikes, but if it is removed, then Terico upgrade suffers (they have free +100% vs mounted).
4. is something that I think was deliberate to stay after upgrade. Another reason why modifying 3. is tricky.
Drawing line after 2. is best bet, since there is blurred line between unit bonus abilities and UU-bonus abilities (Pikemen vs Terico), while there is no such issue with penalties.
EDIT:
Currently, following penalties (as far as I'm aware) carry over after upgrade:
-PROMOTION_ROUGH_TERRAIN_ENDS_TURN (chariot archers)
-PROMOTION_MOUNTED_PENALTY (cavalry)
-PROMOTION_DEFENSE_PENALTY (lancers)
-PROMOTION_NO_DEFENSIVE_BONUSES (lancers)