@YouDontKnowMyName

did you try tap hold the widget and select resize ?

Apex Setting > Home Screen Setting > and adjust the portrait grid size

Certain apps/widgets meant to be use with Touchwiz launcher. If use 3rd party launcher you will coming on out of accurate size. Either you get much smaller or much bigger size.
Dont think can do anything about it though

@YouDontKnowMyName

I may be mistaken but right go to nova settings by the bottom left button on your S3.

then go to drawer. Change the drawer app grid and see if that fixes it :/

So maybe if you set the same grid of apps allowed to be plotted on the screen, then maybe you can get the same look like on touchwiz ? 

Thats my theory.

@YouDontKnowMyName
did you try the desktop settings suggestion in nova prime ?

That previous app drawer was incorrect. Because that had nothing to do with the placement of app icons on the main desktop for android. So my bad

So check if the desktop settings (row/column, height/width) helped you fix this