The cross-staff property, when set, switches off skyline calculations. This leads to various problems in overall spacing.
On/off simply is not sufficient as a value for this property. Instead it should be a pair of systems or vertical axis groups indicating the lower and upper range of the cross-staffiness.
A cross-staff grob will then contribute to the upper skyline of an axis group when this axis group is the same or higher than the grob's upper cross-staff property, and to the lower skyline of an axis group when the axis group is the same or lower than the grob's lower cross-staff property group. That way, cross-staff material will not disappear altogether from skyline calculations but only for those skyline calculations where it should be excluded.