I think the conflict is more cultural than people realize: an office in Daly City is tremendously easier to reach and if you're coming from South Bay -- essentially you exit the freeway and park.
On the other hand, getting to a point in SF from the freeway and parking usually takes at least 30 minutes (in addition to the 30+50 minute drive from the starting point in the South Bay or Peninsula). SOMA area is reachable by Caltrain, but Caltrain is unreliable, doesn't run as frequently nor is SOMA the only place where people have offices (and walking to further reaches of SOMA, or the area of Market, or FiDi is an often dangerous - especially at night - 20-30 minute walk).
Daly City is reachable from SF by BART, but that supposes you live near a BART station in SF and the Daly City office itself is close either the Daly City or Colma BART station. In general I'd say it's easier for an SF resident to get to certain parts of Daly City (those accessible by part or by San Mateo county buses running from SF are easy if you live near BART) than it is from someone in South Bay to get to SF. Driving is very easy if you live near 280/35/19th Avenue -- getting to Daly City from Mission especially is not particularly difficult).
That brings the cultural issue: different people prefer to live in SF vs. South Bay or Peninsula (some live in one place whereas they'd prefer to live elsewhere, of course). To hugely (but completely meaninglessly) over-generalize you can imagine the Peninsula as the OSI stack: physical and network layers are further south, middle-ware is in the Peninsula (Oracle in Redwood City), and presentation (end-user applications like AirBnb) are in SF (again, this is only loosely so: there are web app startups in South Bay and there are systems and middle-ware companies in SF). Intuitively it makes sense: I can't imagine starting a Foursquare in San Jose (there isn't a critical mass of people -- not all of them geeks -- cloistered around any given landmark to gain sufficient traction).
In many types of companies, you want both: which is why companies always seek to locate in either transit accessible parts of South Bay/Peninsula (Mountain View, Palo Alto, San Mateo downtown areas), run buses, locate in SoMa, or have multiple offices (this sounds like a "no-go" for Reddit, but Square, Google, Twitter, LinkedIn, and my own employer -- Cloudera -- all do this). Yet, if a company has a very strong SF-oriented identity (at least for its Bay Area office), a compromise location (especially if the compromise isn't just an SF office near 4th and King) could definitely upsetting existing employees who might also feel that they are no longer as valid as potential new employee the company wants to hire from South Bay.