"I am trying to get the shadows of the trees to match the sun do I need to rotate the HDRI in Treemaker or will it adjust when it renders?"
The appearance of the tree in SketchUp (coloration and shadows) does not effect the rendering of the tree in IRender nXt. The tree will be re-generated and re-rendered.
So, only people who want to use trees directly in SketchUp images, or with other rendering products, need to worry about resolution, direction of sun, shadow masks, etc.
Here is an image of a tree which would have had much lower resolution in SketchUp, but is re-rendered at higher resolution in IRender nXt. The illumination, detail, and shadows on the leaves are recalculated when the treerenders.