If there is a problem with the rental car company you then have to deal with Priceline and the company blaming each other. It's rare but happens. The only thing we ever book 3rd party is, on occasion, a hotel.
IMHO, the $50 savings is not worth it. I'm not being snarky but just pointing out that $50 compared to the rest of the cost of a WDW trip is virtually nothing.