This tool works by storing JSONL in a .beads/ folder. I wonder if it could work using a separate initially-empty "beads" branch for this data instead? That way the beads data (with its noisy commit history) could travel with the repository without adding a ton of noise to the main branch history.
The downside of that is that you wouldn't be able to branch the .beads/ data or keep it synchronized with main on a per-commit basis. I haven't figured out if that would break the system.