Yes, the boost time setting is global and is not customized for each zone. If you use the same controller to drive solenoids as well, you should leave the boost time as is. It won’t cause any harm to your relays because it’s a very short pulse. If this is a concern, you can always have the common wire for relays run separately from the common wire of solenoids, and connect the relay’s common wire directly to the positive wire of the input power supply (i.e. not to the COM terminal). The boosted voltage is presented on the COM terminal, and obviously not on the positive wire of the input power supply.