I live in Philadelphia and this is true there too. In general the city is dense enough that bike commuting is very viable, but the most direct routes are far too dangerous for most people.
I think the challenge is not with the specialized workers, but with the lower paid staff. The cleaners, the cooks, the maintenance crew, the guards. They won’t be able to afford to live near such places because they get displaced by specialized workers, and then they’re stuck in a commuting model.
Clusters of companies already exist. One is Manhattan where finance jobs are concentrated, another (like you say) is Silicon Valley where tech jobs are concentrated. In both, the workers choose to live across a vast area.
I wouldn’t say this is that much of a free choice in Silicon Valley, where housing density is highly limited by regulatory means.