This will pull over $2.5 billion in federal grants from the $79 billion transportation project, which has never been fully funded.

A report released Monday by the High-Speed Rail Authority reiterates the authority’s consistent argument: A tunnel and underground station will not work in San Jose. Business and neighborhood groups worry that the proposed elevated structure will be a huge and unsightly addition to the cityscape. What the report does not say — yet it is being discussed internally by HSRA officials — is that the city’s advocacy of a tunnel option could push the $98 billion high-speed rail line to take an alternative path.