Really not sure I understand your points, especially about someone at level 200 being at Pandora witch/Digesekai, and you think that is strange? (because you think their level is too low?)

If that was your question, let me ease your mind- those players who have low levels, but are further in the quest zones than you, are NOT playing pvp, or tower. (because, who needs levels? You don't get anymore energy/fights for higher levels...) (or in a "worse" case, those girls can still drop from pachinkos also) So they only get exp from the quests, and missions (and who knows, they may not be doing all the daily missions!), and thus do not level as fast as you.
If the "world boss" is the girl on the quest page (princess agate, jennie, princess noemy, etc), those girls are automatic for advancing the quest, but I am not sure how you are relating them to "levels". are you calling quest zones levels, and the player level not his actual level, but the quest zone he is in?

As for points per girl, I have noticed the change you describe- some girls you only earn 1-5 affection, others you earn 10-20, and i have even hit 100 affection drops twice recently (which is great, but it is still annoying to earn 85+ affection items because they achieved over 185 affection- why didn't the 100 affection drop earlier!!!). But those have always been dependent on the GIRL for me (IE, I even had 1 event girl giving me 10-20 each time, while the "regular" girl on the same reel was only giving me 1-5)