Yes - it's different pizza (which makes no sense, but I've read repeatedly on reputable WDW sites and in this forum that it's the case).
If you have the time to make an ADR and have a TS meal at Via Napoli (if you just order a big pizza to share instead of individual entrees, you'll pay no more than you would for a CS meal), it's more than worth it! We were really favorably impressed when we went there for a pizza-and-salad lunch. The thin-crusted Neopolitan-style has some similarities to our favorite New York-style pizza: however, if Chicago deep dish is your preference, you may not care for Via Napoli.