New home builders offer many "personal" type items and the mark-ups are substantial, probably in the neighborhood of 1/3 markup. The only reason to buy through the builder is because you a) ran out of money with down payment and closing costs or b) you just don't want the bother of shopping.
A minor thing to consider: The builder will be responsible for any damage caused by placing items you bought through them in the home.
Some items make a little more sense. For example, things like plantation shutters throughout the home can be installed by the builder. Let''s say the retail is $15,000 (or more) and you know you aren't going to own the home past 5 years or so. $15,000 is only $7-$8 per month but let's go as high as $10.00 per month. $10 x 60 months is $6,000 so you've saved over $9,000. Now when you sell the home with these pretty shutters, it will ad value.
Using the same logic on appliances may make some sense but remember appliances devalue over time (like a car) and ad no value at the sale. In fact, the appliances may be at the end of their projected life and / or obsolete models.
Buy the best lot you can get in the neighborhood even if it means downsizing the home! That will pay the best return when you sell.