The discount rate you'd use for NPV calculations hinges on the cost of capital and the risk associated with each scenario. Since each scenario varies in risk, using varying discount rates that reflect their individual risk profiles is the more appropriate choice.
Your approach for the Profitability Index (PI) depends on the emphasis of your analysis. If you're primarily focused on the most likely outcome, then the PI can be based on that scenario alone. However, considering the three distinct scenarios, a weighted average PI that factors in all outcomes might better capture the project's overall profitability. This method would attach higher weights to the more likely outcome and lower ones to the extreme scenarios, which helps provide a more realistic evaluation.