Another work rule that is likely common (I know it is for all Bay Area systems), is the rule for a break at the end of each transit "run" rather than based on an amount of time. This creates an incentive for transit agencies to schedule ridiculously long routes more likely to suffer from bunching and delays, and also makes it much more expensive to utilize short runs along busy corridors during rush hours. This is largely the reason that there isn't service from Millbrae directly to SFO airport any longer on BART (it's two terminal stations, so for every seven minute run you'd have a fifteen minute required break), and part of the reason that SF Muni doesn't run as many peak hour short lines as it once did - during the short period when you absolutely want as many buses and trains running as possible, any short run equals more time that the buses are chilling while a driver is on a break, even a shorter run would be more efficient otherwise.

BART did run a shuttle from SFO to Millbrae and found that only 150 people a day rode it. That's why it was killed. However, there are a few runs at off-peak times that use the train from Pittsburg to SFO as a shuttle. When the shuttle ran, union rules based on yard shifts were used. So, those operators didn't get a "bonus".