How to flatten the USDs by exporting all layers to a single USD.

1 - Load the given USD in the Sublayer node or Asset Reference node. When using Asset Reference node please make sure to load USD file as an Assmebly (Primitive Kind = Assembly).
2 - Connect the USD Export node and set it with Source = Input Primitives, Save Style = Flatten Stage (Collapse all Sublayers and References)
3 - Set the extension you want, preferably the same extension used in the source file.
4 - Leave the other options as default, hit Save to file, the output should be a single USD* file and not the assembly of payload.USD*, mtl.USD* and geo.USD* and without /textures folder - all textures should be contained within the single USD*.