The reason rents and mortgages in transportation and commute friendly areas of the country are high is because those locations are desirable.
If one enjoys the lifestyle, spending less on transportation and shifting that spending to housing is a net win. That's how I did it, and for about eight of my eleven years in the Bay, I wouldn't have had it any other way.
I left the Bay in 2018 because I got a remote job and didn't feel like I was getting my money's worth from the city life. Pretty clearly, in 2020, much of what makes city living good is gone, but it will come back; whether that's a matter of years or decades is very much an open question.