If in Baan a tax calculation should take place, then the system needs to know whether the base amount on which the tax calculation should take place, should be interpreted as gross, nett or gross over hunderd.
This information is stored on the tax code, which you already discovered.
Your example however with tfacp1110s000 is not a very good one, because there this is not applicable. I will explain why:
The total invoice amount which is at the bottom of each paper invoice consists of net amount, tax amount and late payment surcharge. This amount is the amount which should (per definition) be filled in on the first form of tfacp1110s000. This means that the invoice amount in tfacp1110s000 is per definition a GROSS amount. If you choose tax on header, then no matter what tax code you will be chosing, the tax calculation will always be done by interpreting the invoice amount as Gross. You might say that then also only tax codes of type GROSS should be allowed with tax on header in tfacp1110s000, but apparently the designers did not want to force users to create for each tax code a net and a gross variant.
The other reply about tfacp1120s000 is correct, because if you have tax on line with a cost invoice then the amount in that session is interpreted depending on the tax country/code.