Which combinations of the «Apply Discount On Prices» and «Apply Customer Tax» options are valid?

The single invalid combination is:

  • the product prices do not include taxes
  • «Apply Customer Tax» = «After Discount»
  • «Apply Discount On Prices» = «Including Tax»

http://docs.magento.com/m2/ce/user_guide/tax/warning-messages.html

See also:

How to setup the «Apply Customer Tax» option in accordance with the Russian tax law?