Post History

While writing the question I did find one hacky solution which works, and which I will use unless someone has an alternative.

Create a codebehind file for the theme:

    using System;
    using System.Windows;
    using System.Windows.Media;

    namespace Anonymised.Theme
    {
        public partial class DefaultTheme : ResourceDictionary
        {
            static DefaultTheme()
            {
                var tajawal = new FontFamily(new Uri("pack://application:,,,/Anonymised.Theme;Component/"), "./Themes/#Tajawal");
                FrameworkElement.StyleProperty.OverrideMetadata(typeof(Window), new FrameworkPropertyMetadata
                {
                    DefaultValue = new Style
                    {
                        Setters =
                        {
                            new Setter(Window.FontFamilyProperty, tajawal),
                        }
                    }
                });
            }
        }
    }

Ensure it's used by adding

        x:Class="Anonymised.Theme.DefaultTheme"

to the attributes of the `ResourceDictionary` in `DefaultTheme.xaml`.

Then this will be executed while each application is initialising its own resource dictionary, *before* it creates any windows.