Look at the EIR and Health Risk Analysis linked in the first post. There's a lot of jargon used, but what it looks like to me is something in between a full-scale cement plant and a distribution terminal. It's clear that there will not be cement production from primary raw material - no kiln. Cement and other materials will be produced elsewhere (probably offshore), and will be shipped (probably, mostly, by water) to be mixed into prepared cement products. So there will be grinding and the like going on. Most if not all of it will happen inside buildings, but it won't be silent. How the final product is shipped out (rail or truck) probably depends on where and how far it's going, but there certainly will be more traffic for both modes (a good thing, from a profitability standpoint for the carriers, but not so much for people adjacent to streets and rail lines that are presently lightly or not used). Everything has tradeoffs...

There's a certain amount of NIMBY going on, but in a way it's the city's own fault. Vallejo over the years allowed a lot of residential development, and even built a school, right up against the site's boundary fences. So there's a legitimate concern among those residents about what might be emitted. The Health Risk Assessment, after some feasible mitigation measures related to on-site diesel, concludes that it comes in under the air district's "significance" thresholds for CEQA. That doesn't mean zero emissions.

As a new industrial emission source it certainly does need an air district permit as well as land use authorizations from the city. So whatever happens at the city level (and in the inevitable lawsuits over, at least, CEQA), it'll all happen again at the air district. And BCDC (as a shoreline project it's in their jurisdiction). And the Corps of Engineers for fill and piers and whatever related to wetlands and navigation. Even if these companies win at the local level, it'll be several more years before they can start construction.