Imagine you had an agreement with your local tax authority that they agree for you to pay X in taxes. Then few years later tell you that actually, they were wrong and you have to pay more - you would fight this for as long as possible, wouldn't you?

You can try, you'll probably lose. When the figure is so low it should be blatantly obvious it is wrong you won't get far arguing that you did what you were told and didn't realise something was wrong. When you pay 0.005% tax over a year when the corporate tax rate in the country is 12.5% who can you argue you thought you were paying what you were required? They will try of course and I think Ireland and Apple have both said they will appeal to the European Court but I don't think they'll get very far.

Not if you knew the deal was sketchy from the start. What's likely the case here.

Heavy discounts are usually given for this kind of issues by fiscal authorities, unless there is proof (beyond doubt) there was unlawful intent to not pay those taxes.

But this is not a case of a Tax authority asking a company taxes, it is the EC saying what it is the amount owed.