Well, the problem you describe is present within nations as well. Any small business faced with competition from a significantly larger one is in trouble. The government is not able to solve this problem at this time.

However, for example, if the tax law had been written more carefully, M&S would not have won this case. The power of the EU is that the market is big enough that companies will submit to the law in order to make some money. If it works in safety testing, it can work in tax law.

Obviously it's an imperfect solution, but it's a start.