The thing that writers and show runners could not predict at the time the prior season Gene scenes were shot was the specific month and year they occurred. I think they just went with "bleak, cold, hardscrabble Midwestern winter" because it lent itself better to describing the misery of Jimmy / Saul / Gene's life.
When they planned for S6, my guess is they saw an opportunity to wrap the Gene timeline up in a way that need temporal context with the end of BB, the death of Walter White, and Jesse's escape to Alaska. Based on "Nippy", these events in Omaha occurred just a month and few weeks apart. Maybe that will have meaning in the final three episodes, maybe not.
These writers are not lazy, but they will use creative license in an effort to set the feel they want. And to end the series, I can see where they had to just deal with decisions made way back in Seasons 1-5. So, yes snow on the ground in October. Rare, but plausible. The "OMG, it was 60 degrees and sunny that week according the Weather Underground!!!!" takes are just kinda silly. Just nit picky crap that doesn't matter.