> For instance, if I am a citizen of Japan, live there, and run my remote business from there, but the business that I run exclusively makes money from people in Portugal and Brazil, it would be true that my revenue is being generated in those other countries
That really depends on the nature of your business. If you're hosting a web application in Japan then I'd argue you're still doing business in Japan. Same if you're a contractor for companies or individuals abroad. A grey area is if you host an application abroad. You technically do business abroad, but it's unlikely anybody will come after you for tax.
You clearly owe tax abroad if you operate legal entities that are incorporated abroad. Then we enter the vast and diverse field of how to (ab)use taxation and corporate law of different countries to structure your business to avoid as much tax and bureaucracy as possible. How much of that is morally appropriate according to the points you raised is a whole different question.
Disclaimer: I'm neither a lawyer nor a tax advisor.