Yes, that is basic math, what are you trying to say? The tax is 20%, it's not 25%.
You complaining about that sounds like you're complaining that France officially states its VAT rate is 20%, but when you buy something for €120, the included VAT is €20/€120=16.67%.
The confusion with Estonia is simply due to the fact that the tax payment is deferred. They cannot say that the tax is 25%, since it's not a withholding tax.
And as others have pointed out, it's like saying you earn a salary of €10k and you pay €4500 tax, so you receive a net salary of €5500.︀ Then the tax rate is 45% and not 81%. It doesn't make sense to calculate︁ the tax in relation to a net amount.