Non-integrated / Seperate Webstore - Has Anyone built One?

We are interested in hearing if anyone has succesfully built a non-integrated webstore that works with sales order translation software that puts sales orders into Netsuite. 

My experience has been that it is best to always work within the parameters of the system, but we need more functionality and we are left at the moment with very few alternatives.  The Skyytek white paper re webstores and NS suggests that it is a very bad idea - any further thoughts Ray?

A 3rd party inegration  specialist / NS consultant has suggested that they can build this type of non-integrated store for us, although the price tag is certainly an eye-opener.   Any insights from the user group or NS would be very much appreciated as we look at our alternatives.  Our most important need is multiple ship to capability and more flexability with the communication of shipping options and arrival dates of gifts.