There are several historic homes right across from the station. My understanding is that some of these historic homes are on the railroad right-of-way. In most areas, houses in the right-of-way could be torn down or moved so the project to double-track the Los Angeles - San Diego rail line could progress. Because of the historical significance of these homes, it is highly doubtful that any action will be taken to double the tracks through the San Juan Capistrano station.
The photos in this slide show were taken in the mid-1990's by Steve Grande on his Amtrak travels throughout the nation. The size of the photos is purposely smaller as disk space was expensive and download speeds were slower at that time.