I guess we are missing the concept of adjustment on the tax line and on the tax code.
I do not think it is really possible to have it filled automatically because the definition of “adjustment” may vary by country. Also it is quite exceptional operation that requires anyway the intervention of an accountant.
So the accountant would have to edit the tax line on the generated move and activate the adjustment flag.
But we could eventually also add the flag on the invoice line and invoice tax.