Lilly when the builder is making a home just for you, they will want to have some of your money in case you can not go through with the purchase. In this current environment most builders need to draw on a line of credit to build your home and their lender may have put additional requirements on them. There is a builder in my area that does a lot of bussiness and 2 years ago they could build a home with a 5000.00 deposit. last year it was 3.5% of the contract price, now it's 5% of the contract price.
You can try to negotiate the deposit amount with the builder, but the builder will most likely want some sort of deposit with your offer and after signing P&S just like any other seller. If you are requesting custom modifications to a home that hasn't been completed yet, they may require a higher deposit.