The engine is made of of several modules that overwrite each other when they are loaded. The main "engine" is the kernel that manages multitasking, the loading of modules, and access to low level functions. There isn't a "bare" engine par se. Each module can be thought of as a small "meta program" with it's own psudo-engine inside it (Like chocobo race, or the field system)
And example. the .MNU files are not data. Those are actual PSX executable fragments that are loaded by the kernel and ran directly on the PSX CPU.
The whole system is a geared-up state machine, which acts on the data in the savemap. You can make a "template" for the game data I guess. A blank scene.bin, or an empty field file for example. But much of the game is hard-coded in the modules. That's why you hear us say "we have to edit the executable to do A, B and C" all the time. During development, each module could be ran alone with a "stub" kernel, so the field people and the battle people and the minigame people could all work independent of each other.
The PC version crammed the modules into a single hard-coded executable. When they made Parasite Eve (The next game that used the engine) The took the kernel and hard coded other modules for that game. It's why FF7 and FF8s field language is so massively different. The tore down the old field module and rewrote it. The Kernel was also updated to deal with movie overlays better. (That was perfected in 9)
FFX actually uses a modded version of the Vagrant Story engine.
Strangely enough, FF7 is actually based on the Xenogears engine. They forked early in development of each.
So to answer your question, the only way to get FF7 back into it's "developer state" is to have the C++ source code and write custom stub kernels for each module group.
You might as well rewrite the engine.
