I am not trying to complicate your assignment but think your problem out step by step and understand what your client seeks. This, in turn, should drive your Scope of Work. Does your client need market or leased fee value? With 5-years remaining on the lease, I suspect value is subject to the lease (unless there are hypotheticals). Michigan is correct. You need to tell us what the end goal is. If it is market rent, then base and overage rent combined, may exceed market, not fall short.
If it is leased fee, percentage rents are tricky. Did overage occur one year or is there a stable history of overage? If a history exist there are two tools; a) adding the numbers and dividing them by overage square footage, for a one year snap shot, or b) discounting amounts over the term (just as you no doubt suspected). The correct selection should be market data driven based on which method is more credible. We do not know which because we do not have all of the data you possess. If you have cap rates or can support cap rates better than yields, I would add the data and capitalize it. If you have similar caps, from similar situations, the rate takes into consideration, rents going up or down at the end of the term. It is that simple. If you do not you have to gaguage the risk related to overage. We can not do this because we are not familiar with your market situation.
Of course, I am not sure how flexible cash flow stands and my answer is based on some sort of stability (meaning overage is fairly consistent). Either way (discounting or direct cap) is correct, again, it is a decision as to credibility rather than an exact process or the tools used within the process. While this is true of all appraisal problems having multiple tools, sometime returning to the goal (Scope) and the methods credibility can answer a lot of questions. Good luck