^- THIS. And to be fair, it's probably nearly always the right decision for a startup that has no idea if it will even be able to put out its first product. Sinking like $300k into an office build-out of any kind before you hire your first key staff would be nuts.
So a startup pretty much automatically is gonna start out looking like what you described in #2. And the inertia keeps them with that setup even after they have the funds to do it right. AND then the big companies wanted to "skin" their environments to look like a startup - so they opt for commercial open office furniture that, while the costs are still dramatically more than the IKEA route, usually offers little actual advantage over the $60 tables and chairs of the real early-stage startup.
If I build a startup that gets to the stage where I'm hiring people, I'm going to consider providing offices (private or shared) for my engineers, as a way to attract talent.
I'm surprised more employers aren't doing this. Yes it costs more but (1) you get a lot more output out of your employees and (2) it helps you hire and retain good employees.
1. After choosing an office setup, a company is not likely to change it unless it needs to
2. You can set up an open office in an afternoon. Buy some desks and chairs from Ikea and let people arrange them
3. On the other hand, I wouldn't know where to start in order to procure cubicles/private offices.
4. Also, setting up cubicles and private offices involves some construction work. So it takes longer
Also: open offices may be used to try to create a culture of openness and egalitarianism (if even the managers are made to use desks).
For large companies, the reasons above don't make sense, but they do for startups, in my view.