var assemblyName = new AssemblyName { Name = "AssemblyName" };
var assembly = AssemblyBuilder.DefineDynamicAssembly(assemblyName, AssemblyBuilderAccess.RunAndSave);

var module = assembly.DefineDynamicModule("Module", assemblyFile, true);
var mappingsType = module.DefineType("MainMappingsType", TypeAttributes.Public | TypeAttributes.Abstract | TypeAttributes.Sealed);

MapperConfigurationExpression config = // init;
config.MustBeGeneratedCompatible = true;
Pro.MethodBuilderFactory = r =>
{
    // Anything can be there. You can concat two FullName's
    // if you want to reflect get it, or create a special
    // method that finds a mapper for given <T1, T2>
    string name = ConvertMethodToName(r.RequestedTypes);
    var method = mappingType.DefineMethod(name, MethodAttributes.Public | MethodAttributes.Static);
    return method;
};

var mapperConfiguration = new MapperConfiguration(config);
mapperConfiguration.AssertConfigurationIsValid();
var mapper = mapperConfiguration.CreateMapper();
mapper.CompileMappings();

assembly.Save(assemblyFile);