Bring rice vinegar, apple cider vinegar, sugar, and dried crushed red pepper to a boil in a medium saucepan. Toss together onion slices, bell pepper slices, garlic cloves, hot vinegar mixture, and, if desired, thyme sprigs in a large bowl. Let stand 2 hours. Cover and chill 6 hours. Refrigerate in an airtight container up to 1 week.