Bobby already answered what the lot premium is, and he's right that everything is negotiable. But in asking if it's a junk fee - there's usually a pretty obvious reason why a particular lot is worth more. It might be bigger, or have a great view. Usually, there's a reason why you wanted that lot, and the builder figures you're willing to pay to get it. The thing is, you can't always assume you'll get that much more for your house when you sell it, so don't fall for that line of thinking.
As far as the legality of when they disclose a lot premium, hopefully you knew about it before you signed a purchase agreement contract. If the contract specifies a certain lot, and no premium is mentioned in the contract, then they try to add a fee after the contract is signed, you should speak with an attorney.
A lot of people believe they don't need a real estate agent if they're buying new construction, but having someone go through the contract with you and point out red flags, and to interpret the builder's lingo, can save you thousands of dollars.