I had an idea how to implement this and discussed it with Henkka. It involves using ui controls to rotate the product pivot to correct alignment so that measures match the orientation user wants. This way user can align the product exactly what it looks like and has been measured in a catalog they compare the product measures to. BoConcept currently uses BoundingBoxMeasureTool for generating product measures, StackMeasureTool might resolve some of the measurement issues but I think main problem is the overall measurements in the top-left corner. It's been a while since I used it but I think StackMeasureTool wouldn't resolve the measures orientation problem.
I already implemented the pivot alignment (orientation) to some extent but I don't generally like the end result, especially I couldn't think of a good solution where to place the controls and what they would be.
Is this something we could develop as a platform feature?