Straight AP from items like Deathcap and Lich Bane is better when you know that you need burst to deal with assassins that will get close to you. This also more immediately benefits your team in hard engages.
For the most part you do prioritize Mpen and Mana on Kog though because you primarily want to poke enemies down with your ultimate which already does high amounts of sustained base damage. Some hard engage teams though will necessitate you have burst damage so that priority targets die, hence why I personally agree with RudgimusMaximus that Deathcap and Lichbane are usually ideal lategame items on him.
If the other team however is poke oriented, then you'll want to prioritize Rylais and Liandrys and Void Staff to further beat them in poke wars with your ultimate.