Does the programmer who adds a VAT calculation feature to an accounting program fall under the threat of punishment specified for those who levy and collect taxes (mukus), or is there at least some doubt in that regard?

The programmer who prepares sales and accounting programs for imposed taxes is not responsible for the existence of these taxes. Rather, he is dealing with a reality imposed by the state. The responsibility lies with the rulers who impose them. Taxes should not be imposed except when public resources are insufficient to cover the needs and interests of the Ummah, and then only to the extent that meets the need without injustice.