Skip defaultFontSizes migration for custom origin theme.json files

lib/class-wp-rest-global-styles-controller-gutenberg.php

@@ -336,17 +336,6 @@ protected function prepare_item_for_database( $request ) {
 				$config['settings'] = $existing_config['settings'];
 			}
 
-			// TODO: Figure out where this should actually go.
-			if ( isset( $config['settings']['typography']['defaultFontSizes'] ) ) {
-				unset( $config['settings']['typography']['defaultFontSizes'] );
-				if ( empty( $config['settings']['typography'] ) ) {
-					unset( $config['settings']['typography'] );
-					if ( empty( $config['settings'] ) ) {
-						unset( $config['settings'] );
-					}
-				}
-			}
-
 			$config['isGlobalStylesUserThemeJSON'] = true;
 			$config['version']                     = WP_Theme_JSON_Gutenberg::LATEST_SCHEMA;
 			$changes->post_content                 = wp_json_encode( $config );

lib/class-wp-theme-json-schema-gutenberg.php

@@ -95,9 +95,9 @@ private static function migrate_v1_to_v2( $old ) {
 	}
 
 	/**
-	 * Sets settings.typography.defaultFontSizes to false as it drives
-	 * PRESETS_METADATA prevent_override in class-wp-theme-json.php which was
-	 * hardcoded to false in v2 but defaults to true in v3.
+	 * Migrates from v2 to v3.
+	 *
+	 * - Sets settings.typography.defaultFontSizes to false.
 	 *
 	 * @since 6.5.0
 	 *
@@ -109,7 +109,25 @@ private static function migrate_v2_to_v3( $old ) {
 		// Copy everything.
 		$new = $old;
 
-		// Overwrite the things that changed.
+		// Set the new version.
+		$new['version'] = 3;
+
+		/*
+		 * 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']
+		) {
+			return $new;
+		}
+
+		/*
+		 * Even though defaultFontSizes is a new setting, we need to migrate
+		 * it to false as it controls the PRESETS_METADATA prevent_override
+		 * which controls how CSS is generated and was hardcoded to false.
+		 */
 		if ( ! isset( $new['settings'] ) ) {
 			$new['settings'] = array();
 		}
@@ -118,9 +136,6 @@ private static function migrate_v2_to_v3( $old ) {
 		}
 		$new['settings']['typography']['defaultFontSizes'] = false;
 
-		// Set the new version.
-		$new['version'] = 3;
-
 		return $new;
 	}