If I understand correctly, you are asking if having the lvl 90 ability as the third ability makes it less effective. Please correct me if I’m wrong.
The level is the only thing that effects effectiveness. Rarity, ability position, sprite, family, etc. do not matter. However, I strongly strongly suggest you have electric as your third ability; the third ability gets only a small fraction of the power out of feedpower compared to the first ability (I think it’s like 35% maybe lower. Second ability is 70% I believe). Basically, it will take about 3 times as much feed power to max the third ability compared to the first. It is far more efficient to hatch a pet with electric as third ability. Humanoid eggs can be bought easily for a def each and have a 1/56 chance of giving you h/mh/e or mh/h/e. So, most of the time, you can get the “perfect” combo that will forever effect your account incredibly for less that a deca (unless you are incredibly unlucky). It is infinitely easier to get enough wealth to buy the eggs to get the right combo than to get hundred of thousands of feedpower and the tens of thousands of fame to feed it.
tl;dr No, ability order has does not effect effectiveness, but you should absolutely 100% get the right combo instead of having electric not 3rd