> As long as I don't get taxed on the same money in both countries, I don't see the issue here.

That's exactly one of the current issues. The general rule is something like 'taxation happens where the company creates value'. Registration in Estonia just means taxation starts in Estonia. But at any point can Spain say 'we consider this a Spanish company'. After Spain taxes too, you can request a tax refund in Estonia. That's assuming they agree. Both countries will only communicate with the company, not with each other.

So while double taxation treaties are great, they are not doing much upfront in this respect.

The above is about company taxation, not personal taxes. For SMB that line is often confusing.