I'm not a rail builder but am local to the NWP and have been keenly watching SMART construction progress.
As to the question of why track ballast is being spread by truck (and not by train) in the San Rafael area, note that track reconstruction has been proceeding at multiple fronts. Old track south of Ignacio wye junction has been recently pulled up. Railroad service is north and east of Ignacio, while the San Rafael branch is marooned until its trackage is rebuilt. There are large hopper cars marked with HERZOG lettering currently in use for dumping ballast between Novato and Petaluma. It would seem that using dump trucks to drop ballast is an expedient to the project logistics and schedule demands.
Incidentally, SMART maintains a construction update page on the website at [main.sonomamarintrain.org]
Check it out.