I believe the Feature.ID you would be seeing is the sequence's hash which is a unique identifier for the SV (see here). You could just as easily replace them with arbitrary names like "SV_1" if you wanted. To do that, add an extra column to your taxonomy object with something like:
taxonomy<-taxonomy %>% mutate(SV_ID=paste0("SV_", 1:nrow(.)))
Then paste together SV_ID and Taxon to make Feature.