Onion Architecture isn't about the configuration being implementation-agnostic, it's about the execution.
Just create an IMapper interface for the execution of mappings, but don't worry about the configuration. This applies to your ORM, IoC container and everything else.
Also, Onion Architecture isn't about project structure, it's about the direction of your dependencies. Just call CreateMap in your UI. You can then define an IMapper interface all the way down in Core, with the other pieces implementing a version that delegates to AutoMapper.