$29B over ten years is an annual amount of less than 1% of Microsoft's current annual revenue. Meanwhile the company is appealing it so the government hasn't actually won anything yet (but is incurring additional costs), and on top of that it means there is now going to be a court decision about how this works, which benefits the companies wanting to do it by clarifying the law so that even if they lose the courts will have told them what they need to do differently next time in order to win. Of course, if they win then it's even better for them because then they can just keep doing what they were doing before.

The actual problem is that "transfer pricing" is inherently ambiguous and subject to manipulation but it would take structural legislative changes to the tax code (e.g. tax corporations using something other than corporate income tax) to take it out of play.