The $68 billion figure includes the full length of the line from downtown LA to downtown SF. The segment from Burbank to Merced is just the first one to be built. There are already tracks (albeit not high speed ones) from Burbank to LA and from Merced to Oakland, so when that section finishes you'd still have a one seat ride except for the last five miles crossing San Francisco Bay (for which you'd have to transfer to BART).
