Is there a way to apply SlowCheetah transformations during debug locally without changing the root Web.config? Currently I have the following in my project file

<Target Name="BeforeBuild">
    <TransformXml Source="Web.config" Transform="Web.$(Configuration).config" Destination="Web.config" />
</Target>

This applies the transformations correctly but it changes to the root Web.config. Any changes I make on my current branch to the Web.config now gets mixed up with the transformations changes which is not ideal. I want to segregate my branch changes from transformation changes.

Is there a way to apply SlowCheetah transformations during debug without changing the root Web.config, or at least being able to separate my local branch changes from the transformation changes?