There's the mesh data tool, but that's not something I've used.
https://docs.godotengine.org/en/stable/classes/class_meshdatatool.html
Also consider something more modern, like shaders. This is older documentation but has pictures. https://docs.godotengine.org/en/3.0/tutorials/3d/vertex_displacement_with_shaders.html
I'll just mention, naughty dog in 96 probably didn't have the luxury of being able to load and swap entire meshes like we do, memory has come a long way so it's probably not necessary to emulate that approach directly. Crash 4 uses a lot of advanced shaders for their challenge levels, very talented work they did there. But if you do anything cool with the tool please post- I'm curious to see end result!