Regarding the first floor plan, are you saying no overhead view of the proposed extension is required at all?
The roof can be shown as a "roof plan" or just on your site plan. You would not show the first floor layout unless you are applying for work to the first floor.
I don't think a valley gutter will satisfy a planner in terms of separation. In this context it's visual separation of the two forms - the GF and first floor roofs, and whist a gutter is arguably a physical break, it does not break up the appearance, which is what planners are looking for.
So how would you suggest to satisfy this criteria and provide an adequate break?
If the rear extension roof is lowered and simply rests against the roof slope (and not the rear dormer) would that satisfy it being a separate?