In my Embedded work experience, the BOM costs matters more than SW licensing costs. Which matches the business model of Xilinx.

The company I worked for was selling million or tens of million of units per year. So in such cases it's easy to see why BOM costs trump the SW costs of a few licences, and why HW companies would like to keep chips costs down and charging you per SW license.

If you haven't shipped million of products in embedded and only worked in SW development, it's easy to get a warped picture of reality.