There's a first-hand account out there (RPGLand.com, I think it was) which reports that the load times are in the download version. So, it looks like they really were "wait X amount of time" calls hard-coded into the game, rather than mere "wait for read from CD" calls.
Over a decade ago, a friend bugged the hell out of me trying to convince me to buy a PS2 in order to play Chrono Cross (yes, despite that being a PS1 game), because he was an ardent fan of Chrono Trigger.