Not sure if this is the latest thread on this but this is incorrect -

Let's say the full amount (no voucher) is $200 but with a 20% off voucher is $180. If I pay the amount with the 20% off voucher applied, I expect to be invoiced as such.

It is the reseller (eBay store) that gets the rebate and must account for that, not the purchaser. 

This seems to be a massive flaw in the system for companies purchasing from eBay stores.