This is a full version of the report on the methodology of Human factors, countermeasures for HMI and UX for human and ML model Interaction. Here, the deliverable summarizes progress in enhancing Human-Machine Interaction in Air Traffic Control through user-centred AI design. Task 5.1 focuses on measuring human factors like stress and cognitive load using neurophysiological metrics (e.g., EEG, EDA) to inform adaptive system design. Task 5.2 develops Human-in-the-Loop frameworks using passive Brain-Computer Interfaces to improve AI transparency and responsiveness. The work supports trust, adaptability, and effective decision-making in AI-assisted ATC systems.