I’ve been thinking of something similar! The biggest problem I see is the lack op 3D data in World Machine, as you cannot have two layers on top of each other with height maps. You can have the result of that terrain as a height map, but it is not possible to save the data of plate A going underneath plate B. This would be possible if World Machine were to support 3D data points, kinda like a particle system. That is quite a different approach from transforming heightmaps and would be the best for simulation, as you could give every particle different properties and so have more realistic erosion and such, but at a tremendous increase of computational cost.
I think it is better to create a tectonic plate system in something like Houdini, then create a height map out of it and import that to World Machine.
PS.
My idea is to have different hardness layers in your terrain (again, 3D data). This would make for more realistic erosion and especially “ease” the creation of canyons and such.