I think the idea is that taxes aren't only evaded at the level of the firm. Shareholders also evade taxes, but through "double taxation" they might still end up paying something.
I don’t think the designs of tax structures are that clever or principled. I think it’s more like “we want to spend more and so let’s find the most politically expedient revenue source we can get away with”. Over time, the legislation (and spending habits) put in place by all the politicians that come and go results in an inefficient, inscrutable mess that is modern taxation and government spending, along with requisite anomalies like taxing the same dollar several times.