Here’s the solution. Define this property in your project file:
<PropertyGroup>
<DisableFastUpToDateCheck>true</DisableFastUpToDateCheck>
</PropertyGroup>
PreBuildStep will then execute every time, regardless of whether the project is or isn’t up to date.
It seems that Visual Studio is bypassing normal up-to-date checks of MSBuild and using some sort of custom check that is faster, but has a side effect of breaking customized build targets.