This type of thing happens all the time. In the UK you can work as an independent contractor for years then one day HMRC will randomly decide to make a case that you're were actually an employee the whole time and should have been paying a significantly higher rate of tax.
The UK tax system is not explicit and open to interpretation so these disputes happen all the time if HMRC sees an opportunity. Given government spending is out of control and raising taxes doesn't win political points the complexity and interpretability of the UK tax system is now frequently being used as a weapon against UK citizens and businesses to increase government revenue.
Uber paid their taxes as they understood UK tax law. Not legally complying with their UK tax liabilities as you suggest would obviously be insane. The issue here is that the tax system is designed to be exploited. At least in my opinion. People disagree with me though and believe that the complexity and interpretability of the tax system is done in good faith.
It's a mistake to think this just impacts businesses: https://www.qdoscontractor.com/ir35/gary-lineker-wins-ir35-b...