We've been lobbying for this to be part of IS natively for some time.  In other systems, there is a flag on the shipping method that indicates "will call".  If a will call type shipping method is selected, the system should tax based on the warehouse address.

This would be a difficult plugin (we've looked into it as we need it as well) because of all the places that could (or should) recalc tax (change delivery address, change terms, override tax codes on line or footer, etc.).  We'd have to override of functionality to accomplish a task that's rather simple if done in the core source.

Let's wait and see what the first few hot fixes to SP3 bring.

Thanks,