The author is talking about large defense systems like satellite arrays and airplanes. The status quo that the author is responding to is that engineers of the physical systems (missiles, satellites, etc.) make all the decisions with software bolted on after the fact. This is definitely true at places like Boeing.
You could replace architect with "senior software engineer" or whatever.
Point is, software should have some seat at the table during the design process.
The fundamental thesis of the piece is: "If, instead, system acquirers ensure that systems engineers address software concerns at the same time as the physical solution is conceptualized, acquirers can opt for a slightly different physical system, whose software architecture is tuned to optimize the provided capabilities."
Which, to me, sounds entirely reasonable. If some system needs an MLOC or so and the software will be doing a complex thing like piloting the aircraft, you better be thinking about the software from the beginning of the project...