After you (or your proxy) enter a successful bid, eBay raises the price and increments the bid count. Those are market signals.
It's not a question of whether the auction uses proxy bidding or real-time bid entry... it's a question of when your bid shows up for all to see. It's never in your best interest to call attention to an auction you're interested in bidding on, yet that's exactly what you do when you bid before the very last few seconds.
Are you saying I could buy things on ebay at lower prices by manually entering bids, implementing the auto-bidder algorithm by hand?
Yes, that's what eSnipe and other services do for you. They allow you to hide your interest in an item until it's too late for anyone to rethink how badly they want to win.