Unfortunately this decision has a lot of bad consequences for the main corridor. First, the easterly direction that the train has to take after it gets out of the south bay adds around 20 minutes to the overall trip, which is a substantial fraction of the SF-LA travel time.
The bigger issue is that coming out of Bakersfield, the route is now too far east to make it through the Grapevine. Instead they will have to build a 15 mile tunnel through the San Gabriel mountains which will add more time to the route and cost tens of billions of dollars.
In effect, the choice of route added 25 minutes of travel time at a cost of tens of billions of dollars.
I do believe that Central Valley cities should have rail service, but the main SF-LA route should have been built out first and then spurs or additional lines could have been added to that core.