In case of non-linear transforms you would need to invert the parent transform if you want to define coordinate values in the world coordinate system. As it may not be always possible to invert the parent transform, it's probably simpler to always store and display the coordinate values relative to the parent.

This request has ramifications across all transformable data types. The volume origin/spacing would have to change as well in the Volumes module information widget.
The current system provides the "harden transform" option which will apply the transform to the points and update the coordinates shown in the Markups GUI.

The current behavior has to be changed. Try the following example:

• Create a markups list
• Create a linear transform with a translation of [100, 150, 200]
• Apply the transform to the markups list
• Create a markup by clicking near the origin
• A new markup point is created with coordinates approximately [-100, -150, -200]
• Double-click in the markup point X coordinate and change it slightly (add 0.001)
• Click enter -> the entered X coordinate is changed to -200 => ERROR!!!
• Slightly change the X coordinate again => the X coordinate is changed to -300 => ERROR!!!

This problem was fixed 1-2 years ago.