It's not going to matter. Godaddy already has about 100x the external links that NameCheap does (according to SEOmoz[1] and Majestic SEO[2]). If NameCheap moved up, it was for reasons other than external links.
GoDaddy also has north of 50 million domains registered versus 3 million for Namecheap. If I understand correctly, GoDaddy doesn't make any (or very little) of domain sales, it's the other services like hosting, email, etc that generate the revenue.