The difference: Obsidian is a GUI app for your personal notes; engrym is a headless CLI your coding agent drives, and the KB lives in the repo versioned with the code (or locally if you want to not mess with the repo files).
Two things it does that Obsidian doesn't out of the box: hybrid search (BM25 + local vector embeddings, offline, no API key), and a typed, lint-checked schema (id, altitude, typed relations) so an agent can go from overview to impl detail as a real query, not a keyword guess.
The CLI and schema is the only benefit but I would say they fit agentic coding flows better.
I store my Obsidian in git as well for versioning. There are a few different plugins for that.
I think that Obsidian may not have the schema that you are talking about and I think that it may be missing the hybrid search. It has local search only I believe.
But I do understand that overlap is there and the justification for using a separate tool might be a stretch.