Took me a while to figure this out but here is the solution!
Set up your modular control rig like normal, add your first spine bone or pelvis bone, and the box is giant. In the rig hierarchy on the bottom left panel click your new bone (spine 1, pelvis, etc.) and then in the details you will find - Default → Module Settings → Control size.
For blender models I scale it down to 0.01 and it works perfect! I hope this helps you