I don't know the website you are referring to, but my response is why would you want to use such a service anyway? I have no idea what your level of experience is, but, since you are interested in a kit and want someone else to bend sides and such to a custom shape, I'm guessing you're new to building. Otherwise, you would just create your own body shape, bend the sides, and continue on your merry way. So, with this assumption in mind, I would say to begin with, you will be much better served building a guitar similar in style to one of the numerous tried and true designs from factories like Martin or Gibson. The reason . . . aside from the fact the designs are well tested, you can find great plans from many models that will really help guide you from a construction point of view. If this is you first build, know that using your own body shape creates a number of design issues that you will need to address and resolve to ensure you end up with a decent looking and sounding guitar (think - scale length, sound hole placement, bracing layout, bridge placement, etc., etc.). It is unlikely that a person starting to build his or her first guitar will be have the knowledge necessary to skillfully address and resolve such issues. However, if you go with a standard design and use a good plan, these issues are no longer a problem. Follow the plan as well as you can, and you might just wind up with a decent instrument. The most important thing about your first instrument is completing it.
LMI, which is a sponsor here, has a "kit wizard" that you can use create a "custom" kit package. This may be what you were looking for, though they don't do truly custom pattern work that I know of (plus the whole "dispose of your design" thing doesn't seem to fit). There is a link to LMI at the top of the page, but their website is
www.lmii.com. Great folks with great wood that will treat you right. The kit wizard lets you pick out you top wood, back and side woods, neck wood, etc. You can get a "serviced" kit where the sides come pre-bent to your desired shape ("desired shape" here means a limited number of standard shapes like Martin OM, Dread, etc.), and they include a plan to go along with it as well as Mr. O'Brian's construction video (if you select it as your free gift for using the wizard). If you don't have access to a thickness sander and don't trust yourself with a plane yet, you can have them join and thickness backs, sides, and top. This is a great way to get started, plus you will get a discounted price on supplies using this method (I think it's like 15% off when using the kit wizard).
Good Luck!