New 'UncookedOnly' modules can incorrectly be included as a build dependency after nativization of a Blueprint asset

To get around this you can manually set the package flags. PKG_EditorOnly or PKG_Developer should work. You can see where they're normally set under CodeGenerator.cpp

I did this during module startup and it seemed to work without issue.
Code:
void FYourEditorModule::StartupModule()
{
    const FString LongName = FPackageName::ConvertToLongScriptPackageName(TEXT("YourEditorModuleName"));
    if (UPackage* Package = Cast<UPackage>(StaticFindObjectFast(UPackage::StaticClass(), nullptr, *LongName, false, false)))
    {
        Package->SetPackageFlags(PKG_EditorOnly);
    }