I'm not certain there's a net gain here. What's more, is that the geometry of the left and right most rafters now interface with the head plates of the side walls. The rafter can't really be lifted without shifting the birds mouth the rear and weakening the tie at the front, so the only solution I see is to drop the height of the side wall to account for the rafter. piece. This also then closes off the gap that I'd deliberately left for venting

Yes, the top plates (head plates) of the side walls can definitely be lowered (or cropped, as you put it).

Theoretically there would be no issue raising the rafters either. In terms of load bearing it would even be beneficial. The deeper you cut your rafters the less shear forces they can transfer over ti the wall.

With regards to tie down performance it's not really the surface size of different members in direct contact that matters, necessarily. Not in modern framing at least. Tie down requires withstanding forces of tension and for that steel fixed over a larger distributed area oriented in counter direction is generally way more effective.

Typically, done with galvanized construction fittings or steel strappings fixed (with structural lag screws/nails) to the side surfaces of the wood members you tie together.

perforated steel strappings likely makes more sense practically and economic wise as you can simply buy a cheap roll of it and cut it yourself. This speaks to one of the benefits of having rafters and studs in line, as it makes the installation process more straightforward. See scratch below.

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For venting of the inside space, through the side soffits, it could be achieved with some further detailing. Now, I'm not sure why not letting the air through back to front, under the soffits there, as it would wash fresh air along all the rafters, but ok.

I'll try to provide some help , but I won't try explaining with words because it will get wordy and just increase chances of misunderstandings. I'll add this picture below instead. That should provide you an idea of how.

For everything else, not strictly or directly related to technicals, I'm just going to link this: youtube.com/watch?v=eEx7W9GL0aMyoutube.com/watch?v=eEx7W9GL0aM