Ebay at least is up front about it, as it is basically an auction house for anyone.
But Amazon and Newegg is in a sense lending credibility to any fly by night reseller from who knows where.
When you buy from a big name store front you expect someone working at their supply end has assessed the product as worth the risk of stocking. But with the likes of Amazon, seemingly anyone can start offering products through them.
Consider for example a recent story here on HN about a USB charger that had a damaged transformer. It was giving out straight 240V (European model) to the USB end.
Newegg does what you mentioned though. They're basically putting you into a wild-west type situation where the merchant can do anything they want to you and newegg will just remind you that you have no protection when working with a newegg merchant.
On the flip side, Amazon and Newegg also handle the transaction processing and anti-fraud, which has a lot of value.