I remember having the same kind of discussion when working on rename and when needed to decide where to put the API and some other things. IMO the problem is that, as I understood it, the general direction is to stop putting things in old-core, so the various refactoring operations should go in Refactoring module, but at the same time old core still contains important API for the model, so we still want to have those operations available there.
I do think that we should discuss about the future direction we want for those specific APIs of the model in the future: to keep them there, or to move them, and if so, where.
Personally I would push for keeping simple direct “core” APIs in old core (so for example, a delete in old core would be a full delete only possible with PR), while complex operations should be all moved in Refactoring: a delete there could be a move to the recycle bin, or a real delete depending on the configuration.
IMO it would clarify both our usage and the future direction of those modules. And in that spirit, I still don’t think that this new configuration is a “core” configuration: it’s a configuration for a complex refactoring operation. The fact that it’s currently partly used in old core for now, is something that should be fixed by improving the module in the future.