I'm not sure if there are answers here, since it's been some time. There seems to be confusion around CFC laws and such. If you live in Portugal and have your company in a country that is Whitelisted, it is not about "what they believe" or "would let you pay less tax". If the system is there, it's legal. Portugal does not have the same policy as Germany does here.
If you have a company in Bulgaria, an office address, with a phone number and employee, Portugal will not come and claim that company due to effective management.
And NHR is 20% on foreign income, but 0% on foreign-sourced royalties or dividends, which is where having an offshore holding company comes into play. Cyprus does not have a clear status, malta is also 'grey-listed', so be wary. Portugal will NOT tax you on your Estonian income, even if there is no corporate tax. It's not that you had 'no-tax'. The fact was that you filed taxes in Estonia, they have the right to tax, and it was 0%. But Estonia is not free, because you have to get your money out somehow. This is where Estonia taxes you (20% on disbursing dividends as of right now). Portugal will not double tax you as receiving foreign-sourced dividends are taxed at 0%.
I'm not sure what is meant by "not offering much in return". It's one of the top 5 safest countries in the world and its government and economy work much better and are trending much better than other popular western EU countries. They invest a lot in tech and their people. Spain and Italy are often compared at the same time, and they have the brand name cities, but that's it. The governments and everything are worse off and don't work as well. If this doesn't bother you, go to Southern Italy and take the 90% tax exemption. It's dead simple and the easiest way to get your taxes down to around 5% effectively.
Probably not the most lucid rant here, but there are a lot of comments here about "i don't think" and "i feel like.." that just aren't facts. Find a lawyer or consultant who actually specializes in NHR and saving money through NHR taxation. I guarantee you will find someone who's helped clients with off-shore holdings. Of course, some depends on your citizenship, where you used to live, and how much you want to stay in one place.