In PRINCE2, issue management and change control are closely related, where issue management is considered a subset of change control. Change control is a broader process that encompasses all aspects of managing changes within the project, including issues that might impact the project's scope, timescales, costs, or quality. Issue management specifically deals with resolving issues that can affect the progress of the project.
References: (PRINCE27 Foundation Handbook, AXELOS)

The Organization theme does not include defining the level of tolerance for each level of the project management team. Tolerance levels are typically set within the Plans theme, which deals with how the project is structured in terms of stages and the delegation of authority within those tolerances. The Organization theme primarily focuses on defining roles and responsibilities. References: PRINCE2 Foundation official study guide and materials.

Similar to question 411, the answer remains consistent for monitoring the progress of a stage. The combination of Highlight Reports and Checkpoint Reports provides the project manager with both high-level and detailed insights into the stage's progress. Highlight Reports summarize stage status for the Project Board, while Checkpoint Reports offer detailed progress updates from the team level.References: (PRINCE27 Foundation Handbook, AXELOS)