Hey, thanks for the detailed report and for linking the prior threads.
This is a confirmed bug. The Agents Window’s worktree creation path was missing the step that reads and executes your .cursor/worktrees.json setup commands. A fix for this has already shipped.
You’re on 3.1.15, and the fix landed in 3.1.16. Updating Cursor should resolve this. After updating, when you create a new agent with the Worktree setting enabled, the “Worktrees Setup” Output channel should appear and your setup-worktree-unix commands should run before the agent starts.
You may also find this related thread helpful, where another user reported the same inconsistency: Inconsistent worktree setup between agent and editor windows