"accounting and taxes are a thing everywhere. EU rules make accounting for companies quite complicated" >> this is the most wrong thing ever. You cannot compare the one click accounting in estonia with german kafkaesk absurdity designed to grind you down. How things are implemented are drastically different in countries even if both in the EU.
If you have a company in estonia but you reside and fully control it from Germany, you might be liable for taxation in Germany due to CFC laws.