If the EU can judge that one country's taxes have been "unfairly low" for the last N years, and take what would have been the tax receipts for the last N years, they can raise a lot more than they do by fines. This is especially true if they decide to do it for all of the businesses in a country, instead of just for a few.
I mean, look, the EU is still a place that is more or less governed by rule of law. All I'm saying is that, if the EU keeps the money, that creates the temptation to abuse it.