In the Transform Each dialog, particularly when selecting a corner of the selection as the origin, the appearance of the objects is taken into account, i.e. if you have strokes on the objects, they will be included in the selection "bounding box", and thus change the origin of transformation accordingly. While this could be the expected behavior, it really should be optional, that is, the orign of the transformation should also possibly be based on the vectors themselves, and not their appearance.

All in all, Transform Each is powerful and very useful, but very much under-designed. There are already other suggestions for this dialog, which are all justified and good.