"Mirroring code structure in design files" doesn't make sense to me if you're designing and building cross-platform. Markup does not necessarily translate to native mobile or desktop code. Design tools should enable speed of ideas before consistency of execution, which rarely requires the rigor or structure of production code. This strikes me as too prescriptive of a requirement.
I would say mirror design structure in code. EG the folder structure of both your sketch files and code components follow the same atomic taxonomy.