But Public Buses are just not seen as first, or even second class transportation in the Bay area, so most people, and certainly the vast, vast majority of Silicon Valley employees, would never consider using them to get to work in conjunction with Bart+Caltrain. They are, at most, used as part of two-segment trip. (I.E. Caltrain + Bus, Bart + Bus).
What I'm really trying to say, is that if the valley had a first class rapid transit system around the bay, so you could eliminate the transfer to caltrain, and just go from Bart -> Bus, it might be a reasonable alternative for a lot more people, particularly with company shuttles that run from the nearby bart station to the office on a regular basis.
Speaking of which - I've been away from the Bay for a few years - have they finally unified the payment of Caltrain/Bart/Buses, or are they still on separate payment systems?
So yea you can use a clipper card everywhere but its still complicated. Also, if you load your clipper card online it will take days to actually appear on your card.
Now I work in SJ and on the days I go in to the office I drive to Caltrain --> Diridon --> company shuttle. It's not terrible, except for the waiting. About 1:30 total commute time each way. With no traffic it's about 0:35 up 101 driving. Even with traffic it's only about 0:45 to drive back to Gilroy from SJ, but the morning commute is so ghastly it's better to take Caltrain.
I think the OP was saying that if you have options, Caltrain is probably low on your list. I would agree. It's not like NYC where you're essentially no more than 5 blocks from the nearest subway station.