I'm still confused, didn't you just basically say "yes, we're building on it" and then in the same sentence basically a "we're planning a 3m distance"? Doesn't that contradict itself? Or are you partly building on it (and on the border) and partly deeper (with 3m or now possibly 6m distance)? With 6m distance it sounds like it might still be possible to have a bay window or something projecting into the area, but probably not a normally wide house. (But it also sounds like a good architect might still be able to work something out? Without knowing the entire property now)
Otherwise, how tall is the shed? (That also partly influences whether this "is under 9m long, therefore doesn't trigger extra setback areas" rule applies or not) and is there a development plan that possibly regulates something about this?
But you already notice, yes, basically it can be that edge construction triggers extra setback areas, but it can also be that it doesn't. Your case seems quite special in terms of the setup and as a layman I wouldn't want to make an assessment there. I would probably ask the architect again why they came to the assessment that 3m is enough and possibly get another expert opinion (or maybe the building authority will come to the conclusion after review that "3m distance is correct")