Consider that it's not just a burden to the company, but also to the tax agency. Imagine being the guy who has to go through the papers (could easily be hundreds or thousands of sheets - my own small company submits around 10-20 sheets per month) and then make a transfer of hundreds of millions of EUR every month. Imagine you make a mistake there... That company definitely has lawyers ready to pick on every little thing you do wrong.

Accounts of businesses and governments are without VAT except for the most generalized cash flow tables. My own government reports both numbers (with and without VAT) in cases where this matters. I'm quite surprised yours doesn't do this. But yes, you're right - in your situation the actually spent amount would be different by the VAT rate.