Spending your day commuting and living in a car dependent hell hole is smarter, just because you can retire a bit sooner? What alternative universe has HN transformed into?
As someone with a long train commute, my train time is basically my non-productive "me time". Read a book, read the internet, take a nap, program on fun, non-work projects. If I'm at home, I'm usually engaged in child-care or house-care of some flavor or another, with very little time for simple idleness.
To your last point: in NYC it's pretty easy to do things requiring "undisturbed attention" on a 45 minute express Metro North train into the city from the suburbs. It's a very different experience from the subway.
As for the other three, I guess I could say that I'm not sure it's realistic to try and budget your time so efficiently that a 30-45 minute commute is intolerable. Many people have commutes for which that's a margin of error on how long it will take them - that sounds like a real problem.
Aside from working from home full time, what kind of commute are you looking to have, and at what distance from work? It's not realistic for most people to achieve a 15 minute commute, so 30-45 in a train really isn't that bad. If it really matters then you could do things on the train that would normally keep you from your spouse or kids at home :)
My friend does the Go Train from Oshawa to Toronto every work day. She spends the time on the train either reading a book or watch a video of a show she is following.
On the way home she will sometimes watch a movie and finish it at home. Time on the train does not have to be work or a vegetable.
Just to add perspective here. Toronto anywhere proper, you have to get on a bus generally, to get to the station. Then you have to take the train south to Union. Then take the GO, East to Oshawa. The entire trip can be done in less than hour, but you are walking between connecting options for 10-15 minutes which limits your "free time."
The idea here is many people want a house and if you aren't DINKs then Oshawa was cheaper in housing a while ago. Now it's almost similar to Toronto cost and rent is nearing.
You can trivially get a 30 minute commute just within SF. I imagine other expensive cities are similar. Living within a few minutes of work is a real luxury for all but remote workers.