I'm not sure if the commands actually /stacked/. I think the game accounted for animation time.
The bigger issue was that the framerate was low and everything took a lot longer than it should've.
(Still my favorite FF game 5ever).
An HD remake of FFIX would actually make sense and be pretty simple to do. I mean... literally, just package all the non-downscaled assets in it and pick a reasonable framerate. I don't think the models would even need to be altered much, if at all.