Hi!
So this was my topic from around a week ago, but wit a generic answer. Perhaps we could discuss it a bit more here. 
I had a real struggle to go around this limitation and had to compromise on UX:
Basically I wanted to assign a Layout to the Main Shop index page, which is different from the product Taxonomy archives. I have realized that this was not possible.
Also, I needed a layout for entire taxonomies, not individual ones. For example a Layout for Product Categories in general.
More use-cases would be custom taxonomies from CPT-UI, that could receive their own layout, etc.
Thanks!