Point 3 and 4 could be solved in Rhino.
You can rebuild the surfaces to have less control points which allows you to tweak the shape of those surfaces by pulling points. MoI however doesn't have that option as most surfaces generated have so many control points that it is not practical to tweak them. This would certainly be a great feature to add to MoI though as it is often difficult to create some of the shapes required in a aircaft using default surfacing techniques and a bit of point pulling would overcome those problem areas.
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