Hello jpg87. His organizational vision for assembling complex structures using Assemly 3 is interesting.
How did you solve the question about the need to connect sub-assemblies through their parts?
I did a test where a part encapsulated in Sub-Assembly1 has 1 DOF for animation and another part encapsulated in Sub-Assembly2 also has 1 DOF. When inserting Sub-Assembly 1 and 2 in the Overrall Assembly, both Sub-Assembly lose their 1 DOF and become a single block, making animation and consequently studying the structure's kinematics impossible.
I can only use your organization strategy in structures that have no movement (set of parts united).