From what I've been able to gather, the concerns seemed to be mainly over possible cross-contamination due to the dressing being a liquid that could stick to other foods and surfaces (such as food trays and tables). It seems like having packaged peanuts is less of a cross-contamination risk (or, at least, it's perceived to be).
Wendy's was previously (and, I suppose, once again) one of the few fast food restaurants that did not feature peanuts among any of their ingredients.
It should be noted that Wendy's menu does feature package tree nuts (cashews, pecans, and sometimes, almonds) in several salads, which again, points to the concerns of the dressing being a liquid. Also, peanuts aren't tree nuts (they're legumes), although about roughly 25% of people with peanut allergies also are allergic to tree nuts.
For those of you who miss the Thai-style peanut dressing, it was produced exclusively for Wendy's, but you can probably now make a good case to Marzetti to produce it for retail. You can contact them via their website here.
