Roelof van Ark, chief executive officer of the rail authority, wrote the letter to correct what he called "a misunderstanding" about the agency's Aug. 6 application for federal funds.
That funding application lays out a "phasing" plan in which most of the construction is focused on the north and south sections of the Peninsula segment, leaving a section from Redwood City to Palo Alto with the existing two-track, at-grade system. The plan uses an unpopular aerial viaduct structure to get four tracks through Mountain View and Sunnyvale.
The plan is apparently a hypothetical scenario being used to obtain the federal funding.
Palo Alto officials last week said they were worried about the prospect of more trains passing through the city, potentially creating traffic jams around the Caltrain corridor and slowing down emergency-response vehicles.
Van Ark wrote in his letter that some on the Peninsula are concerned that the language in the federal application "has pre-determined the outcome of our ongoing environmental review process."
"I want to state strongly that this is not the case," Van Ark wrote. "It is our combined state and federal environmental review process that will be used to determine the ultimate alignment selected for the high-speed train's path along the Peninsula."
That process will see its next milestone in December, when the rail authority is scheduled to release its Environmental Impact Report for the San Francisco-to-San Jose segment of the line. One of the most critical chapters in the document is the Supplemental Alternatives Analysis Report, which identifies the potential design alternatives for the voter-approved rail line.
The report, which the rail authority unveiled on Aug. 5, identifies three, four-track design alternatives for the Peninsula segment that will be further analyzed: aerial, at-grade and below grade in an open trench. The Palo Alto City Council High-Speed Rail Committee briefly discussed these options last week, with several city officials saying they support the trench alternative.
Van Ark wrote in the letter that these options have only undergone a preliminary level of engineering (3 to 5 percent). The December report will "further engineer those options to 15 percent, which will allow for a more thorough evaluation of their impacts and benefits."
"Again, a trench option through many Peninsula cities remains an option to be further studied," he wrote.