It's true; although decanting places like TPC and STC have always sold samples and decants for more than the retail price, per ml, of the fragrance. If they did not do this they would not make a profit from the decanting. Therefore, you have a bottle of perfume, such as a regular bottle of Chanel No.5 EDT, that has been marked up in price twice - once when a retailer such as a department store sells the full bottle, then again when decanters such as TPC and STC buy that and decant from it, in order to make a profit off the decants. This is one of the criticisms that has been made of decanting.
That being said, I don't know how decanters arrive at the particular prices they do for some of the fragrances they sell. I was confused, and a bit outraged, when I saw STC selling 1 ml samples of Prescriptives Calyx for $4.99, and 8ml decants for $33. I'm sorry, but that is highway robbery. You can buy this perfume at bargain basement prices online. Right now there are several 50ml bottles on ebay being sold in the $40 range. I know a lot of people have been saying the prices at STC are better but for me it has depended on the fragrance. TPC sells Calyx samples for the standard $3 per ml which it should be. And even that. as you said, is way more than the retail price per ml for the fragrance.