diff --git a/packages/cli/src/config/settings.ts b/packages/cli/src/config/settings.ts
index 01110d7dd..02de5db0d 100644
--- a/packages/cli/src/config/settings.ts
+++ b/packages/cli/src/config/settings.ts
@@ -288,7 +288,12 @@ export function needsMigration(settings: Record<string, unknown>): boolean {
   return hasV1Keys || hasInvertedBooleanKeys;
 }
 
-function migrateSettingsToV2(
+/**
+ * Migrates V1 (flat) settings directly to the latest version (V3).
+ * This includes both structural migration (flat -> nested) and boolean
+ * inversion (disable* -> enable*), so migrateV2ToV3 will be skipped.
+ */
+function migrateV1ToLatest(
   flatSettings: Record<string, unknown>,
 ): Record<string, unknown> | null {
   if (!needsMigration(flatSettings)) {
@@ -943,7 +948,7 @@ export function loadSettings(
 
         let settingsObject = rawSettings as Record<string, unknown>;
         if (needsMigration(settingsObject)) {
-          const migratedSettings = migrateSettingsToV2(settingsObject);
+          const migratedSettings = migrateV1ToLatest(settingsObject);
           if (migratedSettings) {
             if (MIGRATE_V2_OVERWRITE) {
               try {