Thanks for the details.
Quick answer on User Rules:
- Yes, they’ll work differently. User Rules in Settings → Rules are global, plain text, always added to Agent Chat across all projects. They’re lower priority but more reliable than .mdc auto-apply. Docs: Rules | Cursor Docs
There’s known instability with project rules auto-apply, even with alwaysApply: true. Confirmed here: Rules not being applied as expected
Team is working on it.