(Pixelmator Pro 1.0.9 on macOS 10.13.4 on MacBook (Retina, 12-inch, Early 2015))
Constrain proportions is ignored when a shape is part of geometry (Unite/Subtract/Intersect/Exclude).
1. Draw two circles.
2. Highlight both circles in the Layers pane.
3. Right-click and select Unite Shapes.
4. Expand the shape in the Layers pane and select one of the circles.
5. Ensure that Constain proportions is checked in the Arrange pane.
6. Using the Arrange tool, drag on one of the sizing handles of the circle.
Notice that proportions are not constrained. (Also happens if you try to resize the parent object).
Is something not working like it should? Let us know.