I think Weissman did a good job showing which chains pay for quality in their raw materials and processing. Also, frozen fries will always yield a better result in a chain than fresh cut (due to the variables that you mention).

Now, as someone who is also heavily invested in fries due to my family heritage, I will say that I think that Five Guys got shafted in this analysis. Their buyers spend a lot of time sourcing high-quality raw materials from the best growers in the US (mainly Idaho, and I went to High School with several of those growers). When done well, Five Guys outperforms their ranking on Weissman's list.