There are several problems with bounds calculation in Parent class:

If several visible child nodes are added at once (getChildren().addAll(...)), some of them may be ignored during Parent bounds calculation:
reproducible by javafx.scene.Parent_recomputeBounds_Test.shouldNotIgnoreMultipleAddedNodes

Parent.dirtyChildrenList may be initialized incorrectly which results in incorrectly calculated bounds:
reproducible by javafx.scene.Parent_recomputeBounds_Test.shouldNotCreateEmptyDirtyChildrenList

Adding child inside previously calculated untransformed Parent bounds, will leave the transformed Parent bounds (for example boundsInParent) outdated:
reproducible by javafx.scene.Parent_recomputeBounds_Test.shouldNotSkipGeomChangedForChildAdditionInsideUntransformedBounds

Removing child inside previously calculated untransformed Parent bounds, will leave the transformed Parent bounds (for example boundsInParent) outdated:
reproducible by javafx.scene.Parent_recomputeBounds_Test.shouldNotSkipGeomChangedForChildRemovalInsideUntransformedBounds

Incorrectly calculated bounds have negative impact on other functionality - dirty area management, picking, etc.