Repro Steps:

1) Create a Page
2) Introduce two 128x128 rectangles into the RootGrid of the Page.
3) Select each Rectangle, and apply a RenderTransform to each Rectangle of: Origin: 0.5/0.5, Rotation: 45
4) Using the Selection Tool (V), make the two Rectangles partially overlap eachother.

5) Right-Click on each rectangle, and navigate to 'Path', then 'Convert to path' for each.
6) In the Navigator, select the Path furthest away from the RootGrid in which both were created/Top-most visually , right-click it, and in the context menu, select 'Path', then 'Flatten Transform'.

7) Whilst holding [Ctrl], click on both Paths to multi-select them.
8) Right-click on the Path that was Flattened, and from its context menu navigate to 'Path', then select the 'Unite' Boolean mode.

9) Using the Path Selection Tool [A], select the new compound Path, this will make the Path Points appear. Then, select any Path Point on the Shape.
10) Using [Shift+ArrowKey], press the ArrowKey in any direction.

Observe that the Path does not move in the direction the ArrowKey was pressed.
Thanks to this issue: https://www.noesisengine.com/bugs/view.php?id=3571 . We can use this behaviour as proof that the Path has not been Flattened.

11) Using the Selection Tool [V], select the Path.

Observe how the element's adorner is at a 45 degree angle. We can use this as further proof that the Path has not been Flattened, otherwise, it would be horizontal.

Expected Results: Paths are flattened in the process of being Booleaned, especially if they are being Booleaned with a Flattened Path.