I'd suggest writing the VAT persons name down in a very prominent and accessible place, just in case. They tend to change their minds on such things.
In a nutshell, Zen cart implements the concept of a shipping method based tax, rather than an individual product shipping tax, probably because Sales Tax rather than VAT is used in the USA.
The shipping calc routines simply get a weight, from which they calculate a rate and apply any tax they have been told about. To change this cleanly, one would probably have to also pass the product tax rate in, and apply that instead as a quick and dirty. I'm sure there are more elegant ways to do it.

Chuck