Regarding the finding of wild trout during residency surveys, we don't ignore them, but we do not do population estimates either. As I have described in the past, but is worth mentioning again, we did a different study (statewide) of wild trout population biomass and population densities just before opening day and then repeated this work in the same sites mid-summer of the same year. Population densities and biomass were much higher in the summer, which contrasts directly with what a few have said on this message board...that so many legal wild fish, especially brook trout, are harvested on opening day that it ruins the fishing for legal size wild trout for the rest of the year (Our work indicated just the opposite....some were Class C or B in spring, Class A in summer, and legal size fish were more abundant in summer than in spring...and not because of narrower width in summer). . But I digress.
We would not do population estimates at the same time as residency work in part for the very same reason: because the estimates would be lower than summer estimates, but also because the residency work concentrates on adult fish. Nevertheless, if we find multiple year classes of wild trout in streams where they have not been recorded before, we would record the info (measure the fish) if we could do so without ruining the residency sample effectiveness or we would return at a later date to actually do a unassessed water survey, which could involve a wild trout population estimate if the population was large enough.
Typically, I run 2-man electrofishing crew for the residency work, which means the crew has its hands full just trying to sample and enumerate the stocked trout without dealing with the wild trout. For example, the crew may have to ignore the stream margins (fingerling habitat) in order to keep the adult stocked trout from avoiding the crew/electricity (running past the crew in a downstream direction). When doing an estimate of wild trout the stream margins would be electrofished.