In Germany income is taxed where it is generated, which includes the head of the person running the business. So if you run your foreign company from Germany - which is expect to be the case if you have no physical permanent office in Estonia, where you also have to be regularly present - you home is considered to be an business location and thus you are taxed accordingly.
Note that this only applies to limited liability companies.
If you are a single person with no need for limited liability, just register an individual business (Einzelunternehmen) with your local authority (Gewerbeamt). It’s really easy, cheap and if you need support, tax consulting for individual business is rather cheap as well and worth it if your business generates regular income. Otherwise you can just talk to the authorities, because income from passion projects (i.e. non-regular, without the goal of generating a substantial income amount) is not taxed at all.