AFAIK the source for FF9 PSX (and all the PSX ff games) has been lost as Square just used short term archives
Also, FF9 does not run at a constant framerate. Like all the PSX FF games it runs at various rates, sometimes multiple at a time (example: model animations are 15fps vs 30 for the UI)
In terms of timers, the bios does grant you access to root timers, but these are largely modulated by a hardware oscillator
(Incidentally, the hardware timing component is the reason a chipped PAL console cannot produce good NTSC video. Only a Yaroze can support full multiregion play)
FFIX for PSX would have been written in C (or possibly C++) with PSY-Q. It will not be one program - those games were composed of multiple overlays that are banked in / out over the PlayStation's limited memory.
From what I know the PC release was a port to a new framework, which supports the same script engines, but otherwise is fresh code. This is how it can support mobile, widescreen, Steam achievements etc.
There are a number of timers and things used. But the claim that it runs slower is absolutely false. It’s just perceived that way because it’s “drawn” slower.
Secondly, it absolutely will run slower. Animations will take longer to complete; FMVs will play at a different rate ; controller sampling will be reduced.
My scepticism isn't coming from hearsay or ignorance: I have written PlayStation software, and PSX software is not parallelised, even though it can support threading and cooperative concurrency. The control flow of the title is very locked into the VSync loop, from your first ResetGraph(0) right to your final DrawOTable(*p).
In addition, I have done a bunch of reversing work on the other two PSX games, and they are not monolithic programs. They can't be because there simply isn't enough RAM to store the .TEXT of the entire thing at once. So when you say "the source code", I'm inclined to ask - for which module? The kernel or one of the overlays?
It’s not lost except to maybe Square Enix’s corporate but they don’t know where anything is.