VAT is due on any domestic transportation in the EU (eg domestic travel in Sweden also has to pay VAT). Traditional fare calculation doesn't show the VAT, the pricing needs to be done manually asking for the XS component. Any service fee (like the TSC) for domestic tickets also attracts VAT if the issuing office is charging the fee is located in the same country.
The collection of the VAT is the sole responsibility of the ticket office (Airlines and Agents) issuing the tickets. The issuing office (Airlines and Agents) is also responsible to report the VAT to the tax authorities in the correct way. If no VAT is collected, where this should have been done, the liability lies with the issuing office.