In VTA's press releases, VTA claims that their decision to withdraw the BART project in FTA's New Start process is a tactical move.
Year after year of "not recommended" status given by FTA to the BART project, it is easy to figure out how FTA feels about the BART project and how well this project competes with other transit projects around the country.
Knowing that it will receive another "not recommended" status again when VTA and SVLG is likely to be campaigning for another tax, VTA is withdrawing the BART project from the process to improve the tax's chances for voter approval.
Or more importantly, without FTA close scrutiny under the New Start process, VTA would likely to frontload more local tax dollars for the BART project and then say that there's no affordable alternative to building BART. It is like the Bay Bridge fraud: when enough money is spent on designing a bad bridge, some would argue that it is cheaper to build a bad bridge than to redesign and build a good bridge.
However, it is never too late to get things right, especially in this case.