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But this is kind of the point. San Jose is in many ways a bedroom community for Silicon Valley and the wider surrounding suburbs. It has a downtown in the way that, say, Indianapolis has a downtown, a few towers surrounded by parking lots. San Francisco, even today, is (much) more important to state politics, even though San Jose was once the state capital, many of the state's most significant political figures, incuding the current governor, came through San Francisco. San Francisco is the cultural home of the tech elite who live in the Bay Area, it's home to more michelin starred restaurants, sports arenas, better hotels, international conferences, the most expensive urban real estate in the region (I don't even think San Jose has an affluent downtown neighborhood of detached houses like Pac Heights in SF), more good private schools, more in the way of galleries, theaters, orchestras, opera and cultural venues and so on. Nobody outside America has even heard of San Jose, such that people who live there would generally say they live in San Francisco or the [San Francisco] Bay Area. Minus the largely white and east asian bedroom community (much of which is in tech) who technically live within the city's boundaries, San Jose is a largely Hispanic and Vietnamese city with almost zero cultural or social significance to the wider state or even country. Wikipedia even makes clear that the 'Bay Area' is officially short for the San Francisco Bay Area, because every substantial settlement in it was built (or largely expanded) around San Francisco's role as the capital of 'The West' since the early/mid-19th century.
So I think it's relatively fair to describe Silicon Valley as part of San Francisco's wider metropolitan area, in colloquial terms.
San Francisco is not, fundamentally, important because of its Michelin stars, ballets, operas, media, literary artifacts, or galleries. It's certainly the best you'll get within 300 miles, but if those things are what you're looking for, you certainly know cities that crush it on all counts. (In state and federal politics it indeed plays a massively outsize role.) No one flies out to San Francisco to see Lohengrin.
What makes the Bay Area Important is tech and capital; without it, San Francisco would be Portland-level in terms of influence. And for tech, until very recently, the epicenter was in Silicon Valley, which is a bit amorphous but I'd call the geography spanning from roughly Stanford on down. Apple, Cupertino. Oracle, Redwood City (some would object this counts, too far north). Cisco, San Jose. Adobe, San Jose. Sun, Santa Clara. Intel, Santa Clara. HP, Palo Alto. Netscape, Mountain View. Yahoo, Sunnyvale. Later on, Google in Mountain View and Facebook in Menlo Park (another relatively northern outpost). Also, pretty much every VC of note has their offices within a mile or so of each other on SHR: it wasn't as if it was San Francisco airdropping money onto nerdy engineers down south. And most of the tech elite live near where they work: Meg Whitman Atherton, Zuck Palo Alto (albeit after a stint across the street from Mission Dolores), Sundar Los Altos Hills. Pac Heights has more names like Getty or Hellman than tech CEOs. Even in terms of schools, the best private school in SF doesn't really hold a candle in prestige compared to those in the South Bay (Harker, Castilleja, even some public schools like Paly or Gunn).
This provided the initial capital and technical skills that underlie San Francisco's nascent technical ecosystem, which only really started in earnest in the late 2000s. SF has a couple of important, successful companies based there (Salesforce, Uber, Twitter, etc.), but the giants only keep relatively small outposts in the city. And, of course, OpenAI and Anthropic are based there, along with a respectable percentage of Google's ML researchers (though most are still expected to take a shuttle down south to MTV three days per week), but it remains to be seen how that will develop.
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Yes, Silicon Valley has a very odd pattern where in some sense San Jose behaves as a suburb to the towns with tech company offices. This does not make the valley a suburb of San Francisco. Nor do any of the other things you've mentioned.
No, it's the San Francisco Bay Area because it's located around the San Francisco Bay. South Bay was pretty much farms, until Stanford built his university (on his former farm). Shockley founded his company in Mountain View, Fairchild was San Jose, Intel in Santa Clara, etc. San Francisco wasn't invovled.
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