In the attached .qml, the two rectangles differ only by the added

Behavior on origin.x { NumberAnimation { duration: 500 } }
Behavior on origin.y { NumberAnimation { duration: 500 } }

to the Scale transform.
Executing it shows that on Component.onCompleted the two Scales values of origin.x/y are different.

On create rect2: 0, 0
On create rect1: 50, 50

This causes a very different behaviour when the x/yScale values are then changed (click to show the animation, also see screenshot).