Normalizing by the user count should help. My suggestion would be something much simpler ie. to try to compare content itself e.g. top 1000 posts from each sub

Normalizing by the user count should help. My suggestion would be something much simpler ie. to try to compare content itself e.g. top 1000 posts from each subreddit, and estimate (say) cosine sim + Tfidf. Wouldn't that be a better indicator? Also, instead of pairwise comparison, you could try clustering (HDBSCAN for example) to reduce computational complexity. But great work, love your visualizations!