Interesting!
Personally, I actually like having words/concepts with different meanings/applications. As the graph develops you naturally start to see the various meanings bundle and group together (because the related branches also connect to each other) and you end up with an hourglass type shape with the main word being the center, but you’re right that it may not be worth much value for things like carbon, which is very specific.
Have you thought about keeping your definition style notes in a separate folder, so that you can hide them in the graph view with a query? Perhaps it adds a bit of complexity to your vault but might be something to consider