If its an option and they don't exhibit any bias towards candidates that prefer a traditional interview then thats fine, but they should make it clear in the article.
Founder here. We definitely don't and the outcome of both tracks will be treated exactly the same way. As Ammon wrote it: "Anyone who passes our take-home project assessment will get exactly the same service from us as people who do the regular interviews. We'll work hard to find several YC startups they'd be a great fit for, fast track them through the hiring processes, and handle all logistics of flights/accommodations/scheduling."