Comparisons of Generative AI (GenAI) learning interventions raise an important methodological consideration regarding instructional structure. The structural fluidity of AI interactions may introduce uncontrolled variability that confounds between-group comparisons. This is a sharp instance of a broader threat to validity in learning evaluation experiments, where the surrounding instructional structure often remains unspecified even when a particular research element is being tested. Confounders such as instructor delivery, the clarity of an opening explanation, or the form of practice may systematically bias inferences about the manipulated variable. This commentary proposes a four-phase framework (Establish Relevance, Technical Details, Intuition, and Practice) for aligning the instructional structure of learning evaluation experiments. Using the teaching of recursion in computer science as a case study, we demonstrate a procedure for standardizing each phase across conditions. We then examine how the probabilistic nature of large language models complicates, without invalidating, structural control in GenAI research, and we identify practical strategies for converting stochastic output variance from a structural confound into bounded measurement noise.



