I think there is a communications issue here. Those of us who have dealt with the CAA as FTOs and/or AOC holders are used to having a two way dialogue with our TIs and FOIs. Consequently, we are content with bashing around concepts and ides when developing manuals.
Conversely, the conversion of RFs to ATOs will inevitably be the first real exposure many people will have beyond the old system of firing in a load of application and registration forms. The are used to clear regulation and generally accept the CAA's own interpretation of such regulation rather than offer their own means of compliance.
Maybe it would be worth RFs being allocated a specific TI who could then help to build that relationship? Of course, the word is that there are a severe lack of TIs.
Mickey, you will need specific approval for both. For example, the MEP to SEP route would require you to define a class rating 'course'. Not complex, just make sure you list all the approvals you think you will need on your initial application and then talk through with your TI or a friendly flying school.