So what I have found is if I set the X and Y to the global position on my PathFollow3D node, and the Y to the position on the enemy scene itself, it will take the 1 meter offset into account.
I think for the purposes of my game, this will do. But I will definitely look into Raycasts if I have this problem in the future. I think that is the most straightforward path.
Not to draw this out, but one last thing: Is there no way to change the pivot point on a 3D node? Seems the only way is to re-parent: Change Anchor Point of 3D Object - #5 by thatblockypenguin
I could also just do as you said @neozuki and offset the mesh and collision.
Okay, my problem should be solved here. Thank you!