In this case, the issue is what happens to non-tech businesses in downtown. When there are a large supply of small and medium professional services business, the bars, restaurants, barbers and small shops do well. The Palantir employees tend to eat in their own cafeteria, and are perceived to purchase less from the local businesses. This is why there's an element of the population that prefers smaller businesses whose employees go downtown during the lunch hour.
The city does have space though, they just choose not to build on it. Another research park could be built and zoned for. (As could more housing)
The article also doesn't quote the many Palo Alto residents who like being a short commute to work, rather than taking Caltrain to SF for tech jobs.