The trapunto batting spheres could be in either area, depending on what you are going to do for stitching.
If you will be using dense stitching outside the sphere, and quilting right up to it tightly, then let the batting sphere be a smidge bigger, perhaps 1/8" so you catch it with your quilting.
If you will not be stitching tightly up to the edges of the spheres, but will be stitching on the spheres themselves, very close to the edges but still on the sphere fabric, then make the batting the same size. The top stitching will keep it in place.
Spray basting the batting spheres in place will help prevent them from shifting as you work on and around them.
I personally prefer the slightly larger batting with the denser stitching around them... it will make them pop more.
HTH!
And yes Philippa Naylor is one of the queens of trapunto and her show is excellent!