The problem is that the ipad has a different number of icons in portrait and landscape views(4 & 5 respectively).
So, you can use springtomize to make them equal.
Select springtomize in the settings app>icons>use custom number.
I recommend 5 icons per row in both orientations, and everything should be alright.
Note that in the portrait view you may sometimes notice the icons slightly sliding horizontally to accommodate the new customization, this is the only side effect, but it's tolerable.
Would love to hear if it worked for you.
P.S. As for making different icon arrangement for each orientation, I think that's not possible right now, unless there is a tweak for it.