Forgive me if im wrong, but as long you don't receive a salary (or money transfers in general) from the Estonian company entity, you should not be paying any personal taxes in Germany since all the money remains in the company?
This is absolutely right, you don't have to pay personal taxes in Germany if the money remains in the company (it may be a little more difficult, but in essence this is correct).
The company however would have to pay company taxes in Germany.
