diff --git a/wp-includes/class-wp-theme-json-resolver.php b/wp-includes/class-wp-theme-json-resolver.php
index db4b766b82..2048304fdf 100644
--- a/wp-includes/class-wp-theme-json-resolver.php
+++ b/wp-includes/class-wp-theme-json-resolver.php
@@ -525,18 +525,14 @@ class WP_Theme_JSON_Resolver {
 				isset( $decoded_data['isGlobalStylesUserThemeJSON'] ) &&
 				$decoded_data['isGlobalStylesUserThemeJSON']
 			) {
+				unset( $decoded_data['isGlobalStylesUserThemeJSON'] );
 				$config = $decoded_data;
 			}
 		}
 
 		/** This filter is documented in wp-includes/class-wp-theme-json-resolver.php */
-		$theme_json = apply_filters( 'wp_theme_json_data_user', new WP_Theme_JSON_Data( $config, 'custom' ) );
-		$config     = $theme_json->get_data();
-
-		// Needs to be set for schema migrations of user data.
-		$config['isGlobalStylesUserThemeJSON'] = true;
-
-		static::$user = new WP_Theme_JSON( $config, 'custom' );
+		$theme_json   = apply_filters( 'wp_theme_json_data_user', new WP_Theme_JSON_Data( $config, 'custom' ) );
+		static::$user = $theme_json->get_theme_json();
 
 		return static::$user;
 	}
diff --git a/wp-includes/class-wp-theme-json-schema.php b/wp-includes/class-wp-theme-json-schema.php
index 366594ef37..aaa2f968a6 100644
--- a/wp-includes/class-wp-theme-json-schema.php
+++ b/wp-includes/class-wp-theme-json-schema.php
@@ -35,13 +35,14 @@ class WP_Theme_JSON_Schema {
 	 * Function that migrates a given theme.json structure to the last version.
 	 *
 	 * @since 5.9.0
-	 * @since 6.6.0 Migrate up to v3.
+	 * @since 6.6.0 Migrate up to v3 and add $origin parameter.
 	 *
 	 * @param array $theme_json The structure to migrate.
-	 *
+	 * @param string $origin    Optional. What source of data this object represents.
+	 *                          One of 'blocks', 'default', 'theme', or 'custom'. Default 'theme'.
 	 * @return array The structure in the last version.
 	 */
-	public static function migrate( $theme_json ) {
+	public static function migrate( $theme_json, $origin = 'theme' ) {
 		if ( ! isset( $theme_json['version'] ) ) {
 			$theme_json = array(
 				'version' => WP_Theme_JSON::LATEST_SCHEMA,
@@ -54,7 +55,7 @@ class WP_Theme_JSON_Schema {
 				$theme_json = self::migrate_v1_to_v2( $theme_json );
 				// Deliberate fall through. Once migrated to v2, also migrate to v3.
 			case 2:
-				$theme_json = self::migrate_v2_to_v3( $theme_json );
+				$theme_json = self::migrate_v2_to_v3( $theme_json, $origin );
 		}
 
 		return $theme_json;
@@ -100,11 +101,12 @@ class WP_Theme_JSON_Schema {
 	 *
 	 * @since 6.6.0
 	 *
-	 * @param array $old Data to migrate.
-	 *
+	 * @param array $old     Data to migrate.
+	 * @param string $origin What source of data this object represents.
+	 *                       One of 'blocks', 'default', 'theme', or 'custom'.
 	 * @return array Data with defaultFontSizes set to false.
 	 */
-	private static function migrate_v2_to_v3( $old ) {
+	private static function migrate_v2_to_v3( $old, $origin ) {
 		// Copy everything.
 		$new = $old;
 
@@ -115,10 +117,7 @@ class WP_Theme_JSON_Schema {
 		 * Remaining changes do not need to be applied to the custom origin,
 		 * as they should take on the value of the theme origin.
 		 */
-		if (
-			isset( $new['isGlobalStylesUserThemeJSON'] ) &&
-			true === $new['isGlobalStylesUserThemeJSON']
-		) {
+		if ( 'custom' === $origin ) {
 			return $new;
 		}
 
diff --git a/wp-includes/class-wp-theme-json.php b/wp-includes/class-wp-theme-json.php
index 79d1c2e968..4547da40b0 100644
--- a/wp-includes/class-wp-theme-json.php
+++ b/wp-includes/class-wp-theme-json.php
@@ -747,14 +747,14 @@ class WP_Theme_JSON {
 	 *
 	 * @param array  $theme_json A structure that follows the theme.json schema.
 	 * @param string $origin     Optional. What source of data this object represents.
-	 *                           One of 'default', 'theme', or 'custom'. Default 'theme'.
+	 *                           One of 'blocks', 'default', 'theme', or 'custom'. Default 'theme'.
 	 */
 	public function __construct( $theme_json = array( 'version' => WP_Theme_JSON::LATEST_SCHEMA ), $origin = 'theme' ) {
 		if ( ! in_array( $origin, static::VALID_ORIGINS, true ) ) {
 			$origin = 'theme';
 		}
 
-		$this->theme_json    = WP_Theme_JSON_Schema::migrate( $theme_json );
+		$this->theme_json    = WP_Theme_JSON_Schema::migrate( $theme_json, $origin );
 		$valid_block_names   = array_keys( static::get_blocks_metadata() );
 		$valid_element_names = array_keys( static::ELEMENTS );
 		$valid_variations    = static::get_valid_block_style_variations();
@@ -3242,15 +3242,21 @@ class WP_Theme_JSON {
 	 *
 	 * @since 5.9.0
 	 * @since 6.3.2 Preserves global styles block variations when securing styles.
-	 * @since 6.6.0 Updated to allow variation element styles.
+	 * @since 6.6.0 Updated to allow variation element styles and $origin parameter.
 	 *
 	 * @param array $theme_json Structure to sanitize.
+	 * @param string $origin    Optional. What source of data this object represents.
+	 *                          One of 'blocks', 'default', 'theme', or 'custom'. Default 'theme'.
 	 * @return array Sanitized structure.
 	 */
-	public static function remove_insecure_properties( $theme_json ) {
+	public static function remove_insecure_properties( $theme_json, $origin = 'theme' ) {
+		if ( ! in_array( $origin, static::VALID_ORIGINS, true ) ) {
+			$origin = 'theme';
+		}
+
 		$sanitized = array();
 
-		$theme_json = WP_Theme_JSON_Schema::migrate( $theme_json );
+		$theme_json = WP_Theme_JSON_Schema::migrate( $theme_json, $origin );
 
 		$valid_block_names   = array_keys( static::get_blocks_metadata() );
 		$valid_element_names = array_keys( static::ELEMENTS );
diff --git a/wp-includes/kses.php b/wp-includes/kses.php
index 9b998bf6e2..5a1ae2de84 100644
--- a/wp-includes/kses.php
+++ b/wp-includes/kses.php
@@ -2146,7 +2146,7 @@ function wp_filter_global_styles_post( $data ) {
 	) {
 		unset( $decoded_data['isGlobalStylesUserThemeJSON'] );
 
-		$data_to_encode = WP_Theme_JSON::remove_insecure_properties( $decoded_data );
+		$data_to_encode = WP_Theme_JSON::remove_insecure_properties( $decoded_data, 'custom' );
 
 		$data_to_encode['isGlobalStylesUserThemeJSON'] = true;
 		return wp_slash( wp_json_encode( $data_to_encode ) );
diff --git a/wp-includes/version.php b/wp-includes/version.php
index d5cca01ddb..47e0e37bcf 100644
--- a/wp-includes/version.php
+++ b/wp-includes/version.php
@@ -16,7 +16,7 @@
  *
  * @global string $wp_version
  */
-$wp_version = '6.6-beta1-58353';
+$wp_version = '6.6-beta1-58354';
 
 /**
  * Holds the WordPress DB revision, increments when changes are made to the WordPress DB schema.