User Secrets is very useful, but it's only loaded with WebApplicationBuilder, not with WebHostBuilder.
If you're using an existing Startup.cs with WebApplicationBuilder, you can manually create and use a Startup instance.
var builder = WebApplciationBuilder.CreateBuilder(args);
var startup = new Startup(builder.Configuration);
startup.ConfigureServices(builder.Services);
var app = builder.Build();
startup.Configure(app, app.Services.GetRequiredService<MyDependenent>());
app.Run();