A few year ago Caltrans tried to do some improvements to hiway 84 which also shares Niles Canyon. They were stopped cold by the Alameda County Water District which owns the creek and all its water. Seems that the creek is protected by federal mandates to protect the Steelhead trout habitat (not that any get there from the bay) and the cost of working on the road sky rocketed due to the mitigation of the environmental impacts.

I would assume that any changes that would effect the topology would be costly even by ACE and UP standards. UP would not be exempt from the environmental review processes required to straighten the line for higher speeds.

When you read the report, it seems they want a freight only, siding to allow a passing lane for UP frieght trains when the number of ACE train runs are increased. Improving the existing line with ties and rail and surfacing should meet that objective without the need to increase speeds on a short nine mile section of the line.

Again all of this is speculation, NCRY may have moved by then, remember Point Richmond. Other options exist i.e. moving freight traffic through Oakland, actually scheduling the trains both frieght and passenger (like CN did), accepting an operational limit and working with it......

Either way, what ever happens will be 10-15 year from now and for sure things will change before then.