Correct, but there is a BIG but here. Salary will be︁ normally be taxed in the country where you reside, not the country where the payment︂ is made from, but this is just a result of the tax treaty between the︃ countries. Salary will normally be taxable in Estonia if 1) There is no tax treaty,︄ or 2) There is a tax treaty but the country of residence do not tax︅ it.
So, you will have to check the tax treaty to be certain. But, my︆ guess is thatif you do it "your way" you will be taxed in Estonia for︇ your salary.
The way you would normally do this is to register as a sole︈ trader (or similar) in your country of residence. Then you will invoice your Estonian company︉ for services. This will be deductible in Estonia, and taxable in your country in residency.︊