What you saw with a copy of the rectangle being changed but an original image staying the same is a bug and may be Mac specific.
Please create a bug report at: https://bugs.kde.org/
Your description is good and sufficient but a fullscreen screenshot (.png) would be a useful thing to attach to the bug report.
As for using the Transform Tool on a vector object, please see this topic:
Further to that one, if you use the ‘simple’ Free Transform options, you can get a vector object that has different sides having different line thicknesses, which is not a ‘vector thing’.
Use of the Transform Tool on a vector object is unfortunate and strange in many ways. If you really want those many strange effects, you can use a Transform Mask on a vector layer as noted in the linked topic.
If you select it with the Select Shapes Tool, you can adjust its bounding box by the handles with no line thickness variation. But you can do a shear on a vector close to the middle of line handle. A shear operation gives different line thicknesses anyway which is not right for a vector.
The ‘purest’ way to change a vector shape is to use the Edit Shapes Tool to modify the nodes in various ways as given in the Tool Options docker.
Convert To Path will convert a rectangle or an ellipse into a ‘freeform’ vector shape that can be modified in many ways.
Note: It’s always a good idea to have the Tool Options docker visible or readily available all the time, whatever you’re doing.