You may use conditional compilation:
public Startup(IHostingEnvironment env)
{
var builder = new ConfigurationBuilder()
.SetBasePath(env.ContentRootPath)
.AddJsonFile("appsettings.json", optional: true, reloadOnChange: true)
#if SOME_BUILD_FLAG_A
.AddJsonFile($"appsettings.flag_a.json", optional: true)
#else
.AddJsonFile($"appsettings.no_flag_a.json", optional: true)
#endif
.AddEnvironmentVariables();
this.configuration = builder.Build();
}