In this situation, I suspect the default/basic setup for Component Builder is not going to work with this deeper/complicated hierarchy. If you need proxies, than the render/proxy setup from Component Geometry is too simplistic. You'll need the proxy/render purpose geometry to exist underneath the same Xform prims, so they pick up the same transforms.
You can use vanilla SOP Imports to set these up. You can alson set `usdpurpose` attributes in SOPs, to import SOP geometry with a USD purpose already setup; or you could just setup purpose in LOPs. After you have a hierarchy where the proxy/render prims are siblings in the heirarchy, you'll want to set Component Output to "Input Primitives" mode. This makes it far simpler, and doesn't try to use the incoming nodes to make a lot of layers.
You could also decide whether or not you even need proxies. If the geometry is straight-forward enough, it might not be necessary or worthwhile setting up.
