Actually, there are problems in other ways than you think.
I remember discovering in 40d that if you make a save, and embark on a given size of embark on the same area, you would get the exact same embark every time, as one would expect... but if you changed the size of the embark, even just to make the embark smaller over the same embark tiles, but just a smaller area, you would wind up with completely different layers and mineral veins and stagnant pool locations.
The RNG is used for each of these things, so simply revealing different things in a different order changes the outcome of the RNG.
The same random number is being stretched over a larger area, making more calls, which means that when it gets to the same thing, it's already a different number.
In fact, people did experiments where changing the raws to alter something fairly minor, like reactions, would result in completely different world geographies, even though there was nothing in reactions that would have an impact upon the very first thing the game generates.
To get back to the real topic, though...
This wouldn't really help much, anyway. The existence of layer data doesn't slow the game down in any significant way.
What WOULD help is not actually running the caverns until they are revealed. There's no need to have giant cave spiders running wild down there until dwarves are actually capable of running into them.
The HFS already doesn't generate the clowns until you open up the passage. That saves the FPS of having all those creatures.