On seeing your response, I looked to see where "my" D4 was fitted. It was installed on the sloping part of the turret top immediately in front of where "your" hatch is.and therefore I would concur with your assessment.

In so far as clear parts are concerned, I think there is no right or wrong way, and I would go with what you are most comfortable with. For my part, I would paint first as it is easier to clean up overspray off the model, and then fit before painting the turret, masking off the cupola itself, rather than the individual periscopes.