I ride Caltrains all the time. I have never been bumped. The main time you would get bumped would be if the the train is the newer style. They only hold 16 bikes, the regular ones hold 32 bikes. Also, if it is the express the conductores will let a few more on if they know you are only going to P. A. The baby bulllet only makes one stop between SJ to PA. On the express train it only takes 20 minutes to get to PA, under 1 hours to SF.
Suburbia here in California does not lend itself very well to " walkable village-y feel of Park Slope" If you ride Calrtrians down form SF is the best bet. Lots of people ride everyday down from SF.