This is really a software thing – by default the software (both Arduino and Dan’s Interval program) assumes that the master valve is turned on before you use any of the other stations. I don’t use the C program (spinklers_pi) so I don’t know if it can do that or not.
However, it would be possible to code up the ability to have the master only tied to a set of specific stations. It would take modification of the base code but wouldn’t be that tough.
Hardware-wise, the system can open all the relays at once if you want, so any combination can be done.