Hammerhead,
While you technically could use this mod, the only advantage you will get is having a single back-end interface for all three stores. You will have to "wall-off" each product set as the "mixed" concept your presenting isn't possible in the modules current state.

I'm pretty sure you can do what you want to do with shipping, but I would have to really look at it to say for sure. If you can do it, you would have to identify and set the correct variables to enable the shipping modules you would like on each store. You would do this by first enabling all shipping modules you would like to use, then going to the admin and going to tools->multisite tools and searching for the shipping module names. You will see something like this (flat of course would be whatever shipping module you're searching for):
PHP Code:
define('MODULE_SHIPPING_FLAT_STATUS','True'); //Enable Flat Shipping 
Then in your includes/config_sites/<STORE CONFIG FILE> you would set that to True or False depending on what you want for that store.

If you don't care about the single backend, then just install zencart 3 times. It would be a lot easier since you're not really getting the true benefit of this mod.