Earlier quoted context omitted.
That's in every EU country for tax and social security reasons, they want you to also be a tax resident there because that dicatates your tax, labor laws and employee benefits meaning it's familiar and predictable for the company. There's no EU wide citizenship, employee regulations and tax liability for employees but are local for each country. They don't want you earning money in one country but spemding it and tax…
You pay income tax based on where you live though. So I can earn money from Germany, but if I live in Estonia, my taxes go to Estonia. Most remote workers I know are set up as LLC's, and they simply invoice their clients for the work, entirely avoiding any tax or social security issues for the employer, since you the employee have to deal with it yourself in your own country.
In your example, at first you pay taxes in Germany and if Estonian taxes are bigger, you pay the difference there.