The tree-ness of parts of a vessel is actually a technical limitation of KSP API and feels counterintuitive from the disassembly point of view, where one should be able to disconnect any physically external part from the more internal part.
To achieve this intuitive mechanics, though, I need to implement in-flight dynamic re-rooting of a vessel that is too be recycled. Which is costly work-wise; and it's not clear at the moment if it's at all possible.