OK, after re-re-reading (that dissent is interesting), the STB declaration turns out to be nothing really new, except in the way it specifically discusses CEQA. It's based on a section of the STB's enabling law, where Congress explicitly preempts state and local regulation for rail lines covered by STB (and formerly ICC). The decision cites several precedents.

Essentially, STB says that CEQA can't be enforced against a specific construction segment, especially through injunctions, once STB has authorized it. That goes a bit beyond existing CEQA exemptions for passenger service and CAHSR; see CEQA Guidelines chez Google, and any number of other CEQA resources especially the Resources Agency web site. Of course, a lot of the up-front CEQA work is also needed for NEPA, which FRA and STB make findings about, so many studies and mitigation measures still have to be done. The federal preemption provision STB cites is specific to STB, so for now I don't think it's likely to be jumped on by other federal agencies in strange and wonderful ways. The dissent pretty clearly states why the commissioner thinks the majority of the Board may be overreaching, but who's going to challenge them?

There are other ways to go after CAHSR, so loss of the direct CEQA attack for STB-approved construction segments will cause some extra work but won't stop the war. This is just the end of one skirmish. But yes, it's an interesting decision that might be relevant for other rail projects in California.