I don't see how you can think this is broken. Think about the implications if it wasn't like this. Bankruptcy would be rampant and R&D investment would be impossible for everyone but the largest companies.

I disagree, as these companies already calculate how much they need to spend to prevent having to pay taxes.

That doesn't matter. They're still spending it, rather than keeping it as profit.

Well yes, governments tend to like their industrial bases growing and are willing to wait for bigger gains over a longer time period. That isn't broken it is by design.

How are they windfalls? For whom?