It appears that there is no proper solution to your problem. TargetType in Styles doesn’t manage derived types.
Here are two alternatives :
You can put a key in your style and apply the style to all your Windows.
<!-- Resource file -->
<ResourceDictionary ...>
<Style TargetType="{x:Type Window}" x:Key="WindowDefaultStyle">
<!-- .... -->
</Style>
</ResourceDictionary>
<!-- Window file -->
<Window Style="{DynamicResource ResourceKey=WindowDefaultStyle}">
Or you can use the BasedOn property of the Style.
<ResourceDictionary xmlns="http://schemas.microsoft.com/winfx/2006/xaml/presentation"
xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml"
xmlns:my="clr-namespace:WpfApplication1">
<Style TargetType="{x:Type Window}" x:Key="BaseStyle">
<Setter Property="Background" Value="#FF121212"></Setter>
<Setter Property="Height" Value="768"></Setter>
<Setter Property="Width" Value="1024"></Setter>
</Style>
<!-- Inherit from the BaseStyle and define for the MainWindow class -->
<Style TargetType="{x:Type my:MainWindow}" BasedOn="{StaticResource ResourceKey=BaseStyle}" />
</ResourceDictionary>