diff --git a/bin/gstack-config b/bin/gstack-config
index a7d67a4f1..01defcef8 100755
--- a/bin/gstack-config
+++ b/bin/gstack-config
@@ -298,6 +298,10 @@ case "${1:-}" in
       echo "Warning: redact_prepush_hook '$VALUE' not recognized. Valid values: true, false. Using false." >&2
       VALUE="false"
     fi
+    if [ "$KEY" = "plan_tune_hooks" ] && [ "$VALUE" != "prompt" ] && [ "$VALUE" != "yes" ] && [ "$VALUE" != "no" ]; then
+      echo "Warning: plan_tune_hooks '$VALUE' not recognized. Valid values: prompt, yes, no. Using prompt." >&2
+      VALUE="prompt"
+    fi
     mkdir -p "$STATE_DIR"
     # Write annotated header on first creation
     if [ ! -f "$CONFIG_FILE" ]; then
diff --git a/setup b/setup
index 973aaeb1d..9d6453882 100755
--- a/setup
+++ b/setup
@@ -1319,10 +1319,14 @@ if [ "$NO_TEAM_MODE" -ne 1 ] \
   PT_DECISION="$PLAN_TUNE_HOOKS_MODE"
   [ -z "$PT_DECISION" ] && PT_DECISION="${GSTACK_PLAN_TUNE_HOOKS:-}"
   [ -z "$PT_DECISION" ] && PT_DECISION="$("$GSTACK_CONFIG" get plan_tune_hooks 2>/dev/null || true)"
+  # Normalize: strip whitespace + lowercase so "YES", "Yes", " yes" from a flag
+  # or env var all resolve correctly (an unrecognized opt-in must NOT silently
+  # downgrade to skip). Unknown values fall through to "prompt".
+  PT_DECISION=$(printf '%s' "$PT_DECISION" | tr '[:upper:]' '[:lower:]' | tr -d '[:space:]')
   case "$PT_DECISION" in
-    y|yes|true|install) PT_DECISION="yes" ;;
-    n|no|false|skip)    PT_DECISION="no" ;;
-    *)                  PT_DECISION="prompt" ;;
+    y|yes|true|install|on|1) PT_DECISION="yes" ;;
+    n|no|false|skip|off|0)   PT_DECISION="no" ;;
+    *)                       PT_DECISION="prompt" ;;
   esac
 
   _install_plan_tune_hooks() {
@@ -1362,6 +1366,7 @@ if [ "$NO_TEAM_MODE" -ne 1 ] \
     # Real interactive terminal with no recorded preference: ask, with explicit
     # consent + diff preview. The read is time-bounded and defaults to "skip" so
     # it can never hang an automated/forwarded TTY (the conductor failure mode).
+    _PT_PROMPT_TIMEOUT=10  # single source of truth for the read + the countdown text
     log ""
     log "──────────────────────────────────────────────────────────"
     log "Plan-tune cathedral: install Claude Code hooks?"
@@ -1386,8 +1391,8 @@ if [ "$NO_TEAM_MODE" -ne 1 ] \
     log "Backup: settings.json.bak.<ts> written before any mutation."
     log "Rollback: $SETTINGS_HOOK rollback"
     log ""
-    printf "Install both hooks now? [y/N] (default: N, auto-skips in 10s): "
-    read -t 10 -r PLAN_TUNE_INSTALL_REPLY </dev/tty 2>/dev/null || PLAN_TUNE_INSTALL_REPLY=""
+    printf "Install both hooks now? [y/N] (default: N, auto-skips in %ss): " "$_PT_PROMPT_TIMEOUT"
+    read -t "$_PT_PROMPT_TIMEOUT" -r PLAN_TUNE_INSTALL_REPLY </dev/tty 2>/dev/null || PLAN_TUNE_INSTALL_REPLY=""
     case "$PLAN_TUNE_INSTALL_REPLY" in
       y|Y)
         _install_plan_tune_hooks
diff --git a/test/fixtures/parity-baseline-v1.53.0.0.json b/test/fixtures/parity-baseline-v1.53.0.0.json
new file mode 100644
index 000000000..d3736bcc8
--- /dev/null
+++ b/test/fixtures/parity-baseline-v1.53.0.0.json
@@ -0,0 +1,633 @@
+{
+  "tag": "v1.53.0.0",
+  "capturedAt": "2026-05-30T18:00:56.209Z",
+  "capturedFromCommit": "352f6a57",
+  "capturedFromBranch": "garrytan/setup-plan-tune-hooks-flags",
+  "totalSkills": 52,
+  "totalCorpusBytes": 3179282,
+  "estTotalCatalogTokens": 4116,
+  "topHeaviest": [
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+      "skillMdLines": 3153,
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+      "tmplBytes": 53240,
+      "descriptionLen": 291,
+      "hasGateEval": true,
+      "hasPeriodicEval": true
+    },
+    {
+      "skill": "plan-ceo-review",
+      "skillMdBytes": 137751,
+      "skillMdLines": 2290,
+      "estTokens": 34438,
+      "tmplBytes": 63461,
+      "descriptionLen": 794,
+      "hasGateEval": true,
+      "hasPeriodicEval": true
+    },
+    {
+      "skill": "office-hours",
+      "skillMdBytes": 118280,
+      "skillMdLines": 2161,
+      "estTokens": 29570,
+      "tmplBytes": 55534,
+      "descriptionLen": 860,
+      "hasGateEval": true,
+      "hasPeriodicEval": false
+    },
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+      "skill": "plan-design-review",
+      "skillMdBytes": 112728,
+      "skillMdLines": 2019,
+      "estTokens": 28182,
+      "tmplBytes": 28717,
+      "descriptionLen": 218,
+      "hasGateEval": true,
+      "hasPeriodicEval": true
+    },
+    {
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+      "skillMdLines": 2212,
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+      "hasGateEval": true,
+      "hasPeriodicEval": true
+    },
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