Amtrak's not terribly fussy about things like that. I believe I've heard of AGR getting fussy if you get an award ticket and then skip a leg which would turn it into a more expensive award (e.g. booking NOL-WAS-CHI as a one-zone award, since NOL and CHI are in the same zone, but skipping NOL-WAS so it becomes a two-zone award), but especially for unreserved trains like the Capitol Corridor (I think it's unreserved, anyway), I don't think it matters much. It might be different someday when Amtrak gets a live, networked way of scanning and processing boarding passes, but with the current method, Amtrak doesn't know exactly what you did with your coupons until long after your trip, by which time it's too late to do anything. So, if Amtrak.com lets you book a multi-city trip with the bus, then you shouldn't have much of a problem, but if it doesn't, I don't think it's too much of a problem to book OAC-SJC-SAL-SJC-OAC and throw away OAC-SJC.

As trainman74 said, the entire complex is one (smallish) building. The buses stop out in front of the building (east side), and the San Jose VTA light rail tracks run on the opposite side of the mainline tracks (west side), and the two sides are connected by a tunnel under the mainline tracks. The stairs/ramps up to the loading platforms of the mainline (Caltrain and Amtrak) trains are off of this tunnel, too, so you can get anywhere pretty quickly. A half an hour is more than enough time, though 10 minutes would be cutting it close (but would be workable).

And no, the system really isn't that complicated. Anything involving multiple agencies always sounds so at first glance, but in practice, it's an easy transition between them all.

To get a glimpse of the station layout and size, check out this Google Maps satellite view. Buses drop off northeast of the building (in the empty bus lanes).

You can also try this link (hope it works) to see a Google Street View of the area. Click the link, then click on the little yellow man, and then turn to the left (directional arrows in the upper left area of the street view scene). You should see the station building and the bus drop off area to the right of the building and the Caltrain in the background just behind the buses.