Booking with multi-city will save on some routes but not on others. Amtrak will give you the through-fare (i.e. as if there were no stopover) if your stopover is less than 24 hours but will charge you the fare for two separate segments if it's 24 or more hours. This has the effect of basically making stopovers impossible on routes with one train per day (since, by the laws of space-time, your stopover would be at least 24 hours). However, on routes with multiple trains per day, if you schedule your stopover for less than 24 hours, you can get the through fare even with the stopover.

You can do this in PDX and SEA because PDX-SEA and SEA-VAC are served by multiple trains/buses per day (and if you time it right, you can still do SEA-VAC on the once-a-day train with less than a 24-hour stopover in SEA).

If you use the multi-city booking to do SBA-PDX, stop over there for less than 24 hours, then book a segment to SEA again within 24 hours on the Cascades before continuing on to VAC on the Cascades or a Thruway bus, you should get the same price as booking SBA-VAC (assuming that same fare bucket is available on all segments; I just did a test booking for March 9 and it worked fine: $107 direct and $107 with <24-hour stopovers and $157 with >24-hour stopovers). You wouldn't be able to include the Bay Area in your stopovers, because you can't continue from there to PDX with less than a 24 hour stopover (at least without booking SBA-Bay Area on a Thruway bus either direct SBA-SJC/OKJ or connecting to the San Joaquins in the Central Valley).

If you can manage to create a workable itinerary, this practice would save you money, but you'd also be limiting yourself to perhaps shorter stopovers than you'd otherwise like. Of course, it doesn't look like the fare difference is that great, so you may very well decide that the slight increase in train costs is worth the extra time in these cities (all of which are definitely worth visiting!).