This is not new and not unique to MeshParts - same for CSG, and even for parts. The more triangles you have clumped in a small area due to heavy meshes/CSGs or just many parts, the more expensive it is to change part attributes.
We are working on a new part clustering system that will resolve this and many other performance problems of the sort, however it literally means rebuilding the clustering algorithms from ground up - while this is work in progress, don’t expect it to ship this year.