I don't see what this scrutinization of stereotypical trendy startup environments has to do with remote working. If a company has budget for it and wants to make its employees comfortable with open space, and the employees like it, it's their business. To suggest that "serious software engineering" isn't occurring because of how you suppose their workspace is setup is, frankly, offensive.
In software engineering, most of the work goes on inside the minds of the developers. Most of the remainder goes on in a keyboard and a screen. If you wanna get down to it, having more whiteboards and less fancy computer equipment is an indicator of better problem solving, not less.
I sit with three 19 inch monitors on my desk at work. At home, I use a 10 inch netbook most of the time. I have not seen a difference in productivity because when I am focused, I don't need screen real estate for more distractions. Everything just tunes out.
If you consider phd-level university computer science research as "serious software engineering" then I'd note that most research labs I came across in my days in academia were largely empty rooms with some tables and some work desks. Most of the students (phd students, mind you) worked on whiteboard and did coding and writing on whatever laptop they had. The workhorse machines w. big monitors were usually time-shared and dedicated to running heavy processing jobs.
As far as working from home goes, it seems you each agree that being comfortable with ones workspace and environment impacts productivity. That said, one is more likely to have a comfortable and productive work environment when it is up to him/her to decide what equipment to use and where, which a home office lends itself to more than an office, especially on a corporate cube-farm level. Sure, some individuals may not be as productive at a comfortable workspace in the home, but that is the individual. Working from home is not for everyone, but those who find they are more focused and productive in the home environment ought to have that choice.
a classroom full of PhDs may be architecturally similar to an open-floor plan startup office, but the quality of sitting in one and thinking is different - mainly, it's quieter in a classroom. Quieter is good for thinking.
The startups I've seen don't particularly use whiteboards.
As far as working from home goes, it seems you each agree that being comfortable with ones workspace and environment impacts productivity. That said, one is more likely to have a comfortable and productive work environment when it is up to him/her to decide what equipment to use and where, which a home office lends itself to more than an office, especially on a corporate cube-farm level. Sure, some individuals may not be as productive at a comfortable workspace in the home, but that is the individual. Working from home is not for everyone, but those who find they are more focused and productive in the home environment ought to have that choice.