Psuedo code for mapping configuration (as below) is not possible since the lambda only lets us access Type IDataReader, wheras when actually mapping, AutoMapper will reach into each "cell" of each IDataRecord while IDataReader.Read() == true:

var mappingConfig = Mapper.CreateMap<IDataReader, IEnumerable<MyDTO>>();
mappingConfig.ForMember(
    destination => destination.???,
    options => options.MapFrom(source => source.???));

Can anyone think of a way to do this using AutoMapper configuration at runtime or just some other dynamic approach that meets the requirement below.

The requirement is to support any incoming IDataReader which may have column names that don't match the property names of MyDTO and there is no naming convention I can rely on. Instead we'll ask the user at runtime to cross-reference the expected column names with the actual column names found in the IDataReader via IDataReader.GetSchemaTable().