> So if you have an Estonian equevilant of a GmbH/AG your company will get taxed by Estonia and your salary by Germany

Estonian CIT is 0%. If you pay dividends (which is not required), or if you pay director’s salary (optional if you’re a one-man company without a ton of admin), those will be taxed in Estonia. If you only pay yourself for your actual services – no taxes in Estonia.

Germany might tax your Estonian company if they determine the company is a German resident. Check with your accountant.

(IANAL)