I just read the ProPublica story and found that

" IRS set out to be bolder and more aggressive. It took the unusual step of hiring a corporate law firm to represent the agency, a step that incensed Microsoft. The company, along with others in its industry, responded by rallying allies in Congress to rein in the IRS."

Private lawyers make a lot more per hour than government lawyers, and probably Microsoft is using some of those also (rather than in-house employees with stock options and other incentives).  But this case is far from being decided, and there is nothing for Microsoft to "pay back" because the issue is whether it should have paid more when the return was filed. 

The $29 billion is a drop in the bucket compared to what American global enterprises have saved by shifting their profits to low-tax jurisdictions like Ireland.  There are efforts being made to close this loophole with the "global minimum tax."  Republicans, of course, are opposed.  So maybe their leader's tombstone will read, "He was a lecherous narcissist but he kept the price of Windows down."