If you want to use Blueprint in a flatpak build, you need to add it as a module in your flatpak manifest.

{
  "name": "blueprint-compiler",
  "buildsystem": "meson",
  "cleanup": ["*"],
  "sources": [
    {
      "type": "git",
      "url": "https://gitlab.gnome.org/GNOME/blueprint-compiler",
      "tag": "v0.16.0"
    }
  ]
}

Then run your normal flatpak-builder command.