The suggestion the Pelli design is history is misleading in the extreme. The only change is construction of the underground "train box" along with the above ground structure rather than in a second phase of construction. I don't know of any plans to make the above ground structure look or function any differently.
By the way, I wasn't aware that the issue of the # of platforms had been resolved but I think the solution is a good one. I wasn't really a supporter of this whole project when it was first being discussed because I never thought having the station on Mission St. vs leaving it on King St. was worth all the money. The city is growing up around 4th & King and, in a sense, by the time HSR is a reality 4th and King will be seen as very much "downtown" (consider--when Grand Central was built, "downtown"--Wall St.--was a long way away too). So I thought, "Let the city come to CalTrain, rather than spending billions to move CalTrain". But we are where we are and having some trains terminate at 4th & King will be a good solution to space constraints, if any, at the new terminal (I remain a skeptic that that number of trains will ever be needed).