I got the VAT Tool working with stock metahumans, What I had to do with some of my metahuman clothing was take it into Blender and disconnect the rig and apply it to one of the city sample rigs and copy over the weights. In the end it all worked out.
This would probably help with merging to one rig as well.
Swapping rigs in blender
I left my components as sperate because I didn’t want to deviate too much from the City Sample Crowd Blueprint. I ended up not using Niagara, I just stuck with all animated Static meshes. It was compromise that I was willing to make for my project.