There was a ton of opposition in the comment letters on the Draft EIR from Alameda County and Santa Clara jurisdictions and individuals on the on any potential fixes in Niles Canyon and the double tracking through Alviso.
There are problems with both proposals that go beyond the normal NIMBY opposition. It will be interesting to see how the CCJPA confronts the Alviso issue since they've decided to put all of their eggs into the Coast Subdivision and will also need to add tracks through the sensitive bay wetlands at Drawbridge. Maybe SJRRC is hoping that CCJPA solves this for them?
As for Niles, it seemed there were a number of alternatives that were and were not explored that could resolve the congestion issues there. Eliminating the Oakland Sub as a through route north from Niles contributed a great deal to the congestion, but it's easy to see how UP could not feel justified in maintaining 3 mainlines between Fremont and Oakland. A flyover at the Niles diamonds would go a long way toward speeding the flow of trains.
It occurs to me that CCJPA may also need to help solve the Niles problem, because they will want to limit UP freights on the Coast Sub, which probably means getting Altamont freight trains onto the Niles Sub through Decoto instead of their current routing through Centerville and Newark.
In any case, it seems the future of the Niles Canyon Railway is secure for now. I will gently point out that this threat had been touted as one of the principal reasons for why GGRM had to find a new home instead of working to stay or merge.