I think most vendors are fairly good about putting the referenced files (textures, geometry, scripts, etc) in folders not within the Library folders, so it's normally okay to do this.

I have organised my Runtimes along these lines without any problems, except for a very few things where the vendor (or provider of freebies - can't complain about that) put the geometry file right in the Figures (Characters) folder. With these I just moved them out to new folders and edited the references.

"If I were a shadow, I know I wouldn't like to be half of what I should be."
Mr Otsuka, the old black tomcat in Kafka on the Shore (Haruki Murakami)