1. Create a new unity project.
2. Install the ProBuilder package. (Window -> Package Manager)
3. Open ProBuilder toolbar. (Tools -> ProBuilder -> ProBuilder Window)
4. Create a new ProBuilder shape. (i.e. CTRL+K or 'New Shape' in ProBuilder toolbar)
5. Duplicate this shape twice, so there are three shapes in total.
6. Enable 'Pivot' and 'Local' in the Unity Toolbar, to the left of the Play button.
7. Select a duplicate shape, and randomly change it's rotation.
8. Select all ProBuilder shapes in Scene view, selecting the one you edited the rotation of last. The handle should match this object's orientation and position.
9. In the ProBuilder toolbar, click 'Merge Objects'.
10. Undo Step 9 and repeat it a few times.

Expected Outcome: Merged objects should have pivot location and orientation matching the last selected object.
Actual Outcome: Merged objects have varying pivot location with each merge attempt. Orientation does not match the last selected object.

GIF attached to demonstrate the varying handle positions after merge in version 3.0.0
Note that sometimes Step 10 needs to be done a few times to see a different handle location.

Reproducible in package versions: 4.1.0, 4.0.5, 3.0.0
3.0.0 is the earliest version I can find.
You may have to use earlier versions of unity to test earlier packages.