Where to validate AutoMapper Configuration in ASP.Net Core application?

The recommended approach (see JBogard's response) is to move this test into a unit test:

public class MappingTests
{
    private readonly IMapper _sut;

    public MappingTests() => _sut = new MapperConfiguration(cfg => { cfg.AddProfile<MyAutomapperProfile>(); }).CreateMapper();

    [Fact]
    public void All_mappings_should_be_setup_correctly() => _sut.ConfigurationProvider.AssertConfigurationIsValid();
}

After digging around in the IMapper interface (and thanks to the documentation link provided by @LucianBargaoanu), I found exactly what I needed.

In ConfigureServices():

        // Adds AutoMapper to DI configuration and automagically scans the 
        // current assembly for any classes that inherit Profile 
        // and registers their configuration in AutoMapper
        services.AddAutoMapper();

The secret sauce is to add IMapper mapper as a parameter to Configure() - the parameter list is dependency-injected so you can reference any service registered in ConfigureServices()

public void Configure(IApplicationBuilder app, ... , IMapper mapper)
{
  ...
        mapper.ConfigurationProvider.AssertConfigurationIsValid();
}

Works exactly as expected.