I'm not sure how I feel about the entire Cross timeline being relegated to "a computer simulation." I mean, Chrono Cross was night and day different from Chrono Trigger, but I believe a large part of that was intentional -- Crono and company, although they had good intentions, created a whole new set of problems by creating the positive future. Part of that means an insanely wild tangent, El Nido and all the events therein, were a direct result of the time traveling from the first game. It's all Balthasar's fault!

I'm guessing your angle is the same to that of
Star Ocean 3 (in which the whole world is a computer simulation and thus an artificial construct, and yet the realism of the simulations renders everyone real and thus they have souls, yada yada yada)...?
So what events would be real that were integrated into the program, and what would be false?