I am not disagreeing with your statements, but these miss the point. The rules are to ensure consistency across all businesses. However companies like Amazon have processes which are designed to specifically maximize the ability to benefit from these rules.
You may argue that this is something that all companies could do and also represents good financial management, but I suspect that many of these internet companies are using artificial structures which do not align with the real world reality of how the company is structured.
The bottom line is that the tax collection models are still based on 20th Century (and before) business model and the Internet has fundamentally thrown that model on its head. It will take years before a new tax model is developed that is able to cope with the way these companies operate.
The issue for me is not the level of tax that is levied, but ensuring that the tax burden for each company/person is fairly distributed. So local companies can compete fairly with multi-nationals.