In many industrial settings, the common and varying features of related software-intensive systems , as their reusable units, are likely to be implemented by a combined set of traditional techniques. Features do not align perfectly well with the used language constructs, e.g., classes, thus hindering the management of implemented variability. Herein, we provide a detailed framework to capture, model, and trace this imperfectly modular variability in terms of variation points with variants. We describe an implementation of this framework, as a domain-specific language, and report on its application on four subject systems and usage for variability management, showing its feasibility.