Personally, I think they should just write down that anything inside the boundary of an incorporated city, built on a site that previously had something on it, is not a project.
In San Francisco and some neighboring cities, every permit is discretionary either directly or through ambiguity (https://law.ucdavis.edu/sites/g/files/dgvnsk10866/files/medi...), but it doesn’t have to be that way.
This is my favorite graph for explaining how I can be pro-environment without necessarily being pro-Environmentalism™ https://books.google.com/ngrams/graph?content=gentrification...
https://www.sfgate.com/green/article/MERCED-UC-expansion-pla...
If anything, that appears to be a successful use of CEQA, where a large and important building project was effectively balanced with the need to protect wildlife without major disruption to the final buildings.