docs(setup): correct settings-scope comments; cover merged hook path

Fix two factual comment errors flagged in review:

• The #1140 e2e test claimed entire status still showed disabled. It did not: settings.local.json (enabled:true) overrides settings.json in the merged view status reads, so status showed enabled; only the committed file was stale. Reword to the accurate symptom.
• setEnabledFlag's doc said it operated on raw content "unlike" saveEnabledState (implying saveEnabledState writes the merged view) and overclaimed a bidirectional sync. Make setEnabledFlag the canonical merged-vs-scoped explanation (one-directional project->local sync), and reduce the other sites to one-line pointers.

Polish: add a merged-view assertion for absolute_git_hook_path (a mutation reverting it to the scoped struct now fails), assert the #1140 e2e leaves no contradicting local override after re-enable, and replace hardcoded line numbers / a truncated finding id in test docs with symbol names.