If you want to move to Europe (which I think was part of the idea of the article), it may indeed make sense to consider where to move. Germany (and one of its startup hubs, like Berlin or Hamburg) is probably not the worst place to be for various reasons, but I've also heard good things about e.g. Estonia.
I don't have backup readily available but I think your statement about the taxes is just plain wrong. Generally I think income is taxed where it is produced and Europe has (no)double-taxation treaties with pretty much any country. Personally I'd still avoid the extra complexity for a startup :-)
And the USA isn't all that much better.
And as they get the information from Estonia, I don't think German authorities will have an issue that the company is abroad. They're used to deal with a lot of UK companies (especially when the UG didn't exist yet), it's not new topic.
The 20% Estonian corporate tax does not apply to salaries for non-residents, but for things like dividends.
P.S. Leapin is a company that specializes in accounting for online businesses looking to establish a presence in Estonia. You can find some more info on this stuff on their website:
https://www.leapin.eu/faq/receiving-funds#what-taxes-do-i-ne...
As far as Estonia is concerned you will not pay any taxes with them until you take out dividends or similar.
Why would you need to explain my business choices to any german authorities? It's none of their business. On top, Estonia is a member of the EU, not some off-shore tax-evasion island.