The entire goal of using an e-commerce solution like these plug-ins is to automate the process … meaning there’s typically no way to intercept the purchase process for this kind of special handling (that would defeat the purpose of automation).
One option you have, though, is to just not list your “odd” products in the e-commerce solution. List them separately (on a special page, in a different section) so that they can be handled separately. This would prevent them from ever being added to the user’s shopping cart and allow regular purchases to occur instantly as normal.
An additional problem you’ll be facing if you try to build this kind of checkout intervention into any e-commerce solution: security. People are wary of buying things online to begin with, and placing this additional step either requires users to a) authorize the purchase twice (once when they’re shopping, again when your sales rep deals with the purchase) or b) provide you license to charge whatever you want after a sales rep handles the purchase.
Option A will be frustrating to users. They want to make the purchase, receive their goods, and be done with it. Option B opens you up to a lot of risk because you become responsible for someone else’s account information.
So while it might be possible to “hook into the process somewhere” with one of these plug-ins, that would be a very dangerous thing to do.