I think the architect (I assume an architect)is perhaps short changing you.
Probably low balled you and everything becomes an extra. All the plans I see list the materials along with a colored drawing of the proposal.
We have a designer who drew up the plans (same way as last year for a major kitchen remodel involving moving load bearing walls). We’re doing it as owner/builder (they hate do it your selfers). He said he’s never seen any city with requirements like this and yes, he’s done many remodels/additions in the City of Campbell over the last 30 yrs. I guess part of the ‘special scrutiny’ by the planning department was to insist we provide paint/roofing samples but not ensure we’re using ‘low-VOC’ materials, that’s for the F’n Building Department.....you can’t even find anything that isn’t low-VOC around here......
I also am a contractor in CA so I fully understand your point and appreciate a properly thought out set of plans. I have been part of too many projects that were bid on a light set and most parties involved ended up taking it in the shorts to some degree. Happens all the time when you work with people you don’t know or work from crappy plans. A good set of plans is better for everyone and well worth the extra money.
In California some of us have been conditioned to tolerate a government that can dictate what paint to use. Some of us can’t take it any more and need to move before they send us to re-education camp. The problem here is not the homeowner, the designer, the manufacturer of the materials or the men who install them. The problem is a government that has way too much power.