I think your description of the upper doughnut application is incorrect. I just put a new oil trap box on my car while I was doing the head gasket. The flat face seemed to fit inside the recess on the block while the box's features seemed to fit the recessed part best.

I chose to put the lower "pipe" on the box first and then the flanged end went against the engine. Here I don't think there is a great difference. I didn't use sealer and so far there are no leaks.

I had forgotten that I had bought seals a long time ago and found the old design parts after I was organizing after the gasket job. The new parts, (green upper seal and rubber flanged part with the metal support) seem like they will work much better. Besides, tightening those clamps even with the intake manifold out of the way would be a "b@#ch".
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'96 965 with 16' wheels at 121K. Had '85 745 Turbo Diesel for 200K.