She's complaining about the flat structure because it was unwilling to accommodate hardware specialists (e.g., a machinist) which her project needed, but which the software-centric crowd just wouldn't hire. The specific complaint about folks like this was that they were poor fits for the culture as a whole, which is almost certainly true as far as it goes: a machinist can't toddle off with their wheeled desk and join a purely software game project, because they don't have software skills. In other words, they can't function the way a member of that culture is expected to. But at the same time, skills in machining, board design, and the like are necessary if you're going to have a hardware project go to completion.
The bottom line is that her project was just doing something different from the rest of the organization, and needed some degree of autonomy --- particularly in terms of really big areas like hiring --- to do it effectively. The flat structure was simply unable to provide that, because that requires that there be a corner of the organization where, say, software devs have nowhere near the sort of influence that they're used to having on, say, hiring as a matter of course.
I don't think being an expert in a field prohibits you from getting hired by valve. Her project comes across to me as R&D where a small team of experts are working with something trying to find an application, while she seems to come across as wanted to scale up and produce something functional now.
From my POV it almost certianly sounded like she actually needed software folks, as opposed to additional hardware, because the nudges from valve were that her project had to actually display some interesting game play before anyone would be interested.
The bottom line is that her project was just doing something different from the rest of the organization, and needed some degree of autonomy --- particularly in terms of really big areas like hiring --- to do it effectively. The flat structure was simply unable to provide that, because that requires that there be a corner of the organization where, say, software devs have nowhere near the sort of influence that they're used to having on, say, hiring as a matter of course.